Docker images should install and use BiocManager.

Hi, in https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/devel_mscore2/builds/d7a4ddb7-52ab-494a-b572-e88142c3d283

* installing *source* package ‘proFIA’ ...
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c UtilFunc.c -o UtilFunc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-proFIA/00new/proFIA/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  : 
  The prototype for class “proFIAset” has undefined slot(s): 'fClasses'
Error: unable to load R code in package ‘proFIA’
Execution halted
ERROR: lazy loading failed for package ‘proFIA’
* removing ‘/usr/local/lib/R/site-library/proFIA’

There is no failure on http://bioconductor.org/checkResults/3.8/bioc-LATEST/proFIA/

Hi,
rocker/rstudio:3.6.0 appeared yesterday.
For release we need a branch R3.6.0_Bioc3.9 The 3.8 release branch was missing the _ (minor cosmetic itch).

Configuration happens in https://github.com/Bioconductor/bioc_docker/blob/master/config.yml
It would be great to cleanup some of the comments and make them more explicit,
e.g. should always be false to should always be false in release, or 'true half the year->true during devel cycle may to october` (or was it the other devel cycle ?) and remove outdated comments (rstudio-daily does not exist anymore ?).

Check if we still want to support use_numbered_branch, which is used in
https://github.com/Bioconductor/bioc_docker/blob/master/src/base/Dockerfile.in#L72
to (optionally) install an R from sources. This does help during the weeks where rstudio:devel
reports the next R version, which has (and will) cause the bioc docker to fail during april,
unless the biocVersion hack is used in our Dockerfile(s). But it would be a very special case,
as we can't be sure our R compilation is consistent with what rocker uses, so I suggest to stick
with the rocker R version in our images always.

Yours,
Steffen

Not sure if that's the right place to do it, but can we add libpng-dev to the Dockerfile files? It's a lightweight addition that some popular package depend on. E.g.:

RUN apt-get install -y libpng-dev

See, for example:

"bioconductor/release_base2:R3.6.2_Bioc3.10"

https://hub.docker.com/layers/bioconductor/release_base2/R3.6.2_Bioc3.10/images/sha256-332dd25610d65354ab8aa60d0d1ab8ca0101639c8e1fe10dccee1b563d0187f9

vs "bioconductor/release_base2:R.3.6.1_Bioc3.10"

https://hub.docker.com/layers/bioconductor/release_base2/R.3.6.1_Bioc3.10/images/sha256-b2a590e545bc2ed8f701711088fdd6efc845691378320c682ecda404e48fd5e0

I think there's just an extra period in the 3.6.1 tag, since all the other tags lack that period.

Package http://bioconductor.org/checkResults/devel/bioc-LATEST/prot2D/
has to be disabled since its dependency samr was removed from CRAN,
causing build failure in
https://hub.docker.com/r/bioconductor/devel_proteomics2/builds/bhjhiv6ojvgp4dvrzoa8vuw/

https://cran.r-project.org/web/packages/samr/index.html

Package ‘samr’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
Archived on 2018-07-20 as check problems were not corrected despite reminders. 

Hi, build logs like
https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/bohdubxhqdbrqffkjcjsyti/
become difficult to grasp due to excessive noise from download progress bar.
It would be great if there was a global option deactivating that in the base image.

biocLite() uses download.file(). According to ?download.file a progress bar is shown
when in interactive mode. Can be disabled with quiet = TRUE. Yours, Steffen

Yours, Steffen

docker run -p 8787:8888 -e PASSWORD=bioc bioconductor/devel_base2:latest              ✔
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] add: executing...
Nothing additional to add
[cont-init.d] add: exited 0.
[cont-init.d] userconf: executing...
[cont-init.d] userconf: exited 0.
[cont-init.d] done.
[services.d] starting services
/usr/lib/rstudio-server/bin/rserver: error while loading shared libraries: libssl.so.1.0.2: cannot open shared object file: No such file or directory
[services.d] done.
rsession: no process found

Issue carries forward to Bioconductor/bioconductor_full#18

Is there a place to see change logs in each version?

@sneumann - as far as I understand, specifying Metabolomics and Proteomics biocViews in the config file is going to pull all packages that have these tags. I think we should specify a limited number of core MS packages; I would suggest we start with

• ProtGenerics
• mzR
• msdata (experiment package)

and then progressively add anything that would be relevant for the metabolomics and proteomics containers.

ERROR building:
https://hub.docker.com/r/bioconductor/release_metabolomics2/builds/bpc6o9gtsf8stohx3jhvecj/

It appears mQTL.NMR can not be installed because its CRAN dependency GenABEL has been removed from CRAN.
https://cran.r-project.org/web/packages/GenABEL/index.html

Can the package list be updated to not include?

I have reached out to mQTL.NMR to report this issue.

Hi, in https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/devel_mscore2/builds/d7a4ddb7-52ab-494a-b572-e88142c3d283
we get

ok <- BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE) %in% rownames(installed.packages())
Bioconductor version 3.9 (BiocManager 1.30.4), R Under development (unstable)
(2019-03-30 r76304)
Installing package(s) 'BiocVersion', 'biocViews', 'ProtGenerics', 'mzR',
...
	‘/tmp/RtmpvBEE7T/downloaded_packages’
Warning messages:
1: package ‘BiocVersion’ is not available (for R Under development) 

Although it looks to be perfectly (well, one warning) availavle:
http://bioconductor.org/checkResults/devel/bioc-LATEST/BiocVersion/

I have rebuilt the base and core devel (R3.6.0 Bioc 3.9) and release (Bioc3.8 R 3.5.1) images. The release_protmetcore2 container is failing. It appears to be do to a TIMEOUT from what I can tell. Please look into this. Because of this failure the release_metabolomics, release_protcore and release_proteomics containers can not be run.

A problem with using the Docker images for day-to-day work is that installed packages disappear whenever you restart the container. I have worked around this by mounting a volume like this in the docker run statement:

      -v /Users/lwaldron/docker-devel-packages:/usr/local/lib/R/host-site-library

Then from within the container rstudio prompt:

.libPaths(c("/usr/local/lib/R/host-site-library", .libPaths())

I have to enter this latter command in every new R session, because I find that docker run flags like:

      -e R_LIBS_USER='/usr/local/lib/R/host-site-library:/usr/local/lib/R/site-library'

have no effect on .libPaths(). The existing .libPaths() directories already contain packages, so if I mount them to a host volume I lose the packages already installed.

Could the Bioconductor Docker containers add a /usr/local/lib/R/host-site-library to the .libPaths(), to facilitate users who would like to keep a persistent host package directory rather than re-installing them with each docker run?

ERROR: absolute paths in ‘libs/Rchemcpp.so’ include the temporary installation directory: please report to the package maintainer and use ‘--no-staged-install’

The docker hub builds get cancelled after about two hours.
Locally devel_proteomics2 builds on a 3yr old workstatin
in about 36:36.04 elapsed minutes. Yours, Steffen

I'd like to see some of the BUILD/CHECK reports
for the packages in the docker images. Currently,
the image creation only succeeds if all packages BUILD,
so it is an all-or-nothing.

One could try/catch the individual installation,
and create the equivalent of the BUILD/CHECK reports.
Is some of that HTML generating code somewhere on github ?

Yours, Steffen

ERROR building:
https://hub.docker.com/r/bioconductor/release_proteomics2/builds/bjyehkw2iv86hvxsggafmkr/

It appears prot2D can not be installed because its CRAN dependency samr has been removed from CRAN.
https://cran.r-project.org/web/packages/samr/index.html

Can the package list be updated to not include?

I have reached out to the prot2D package to report this issue.

As far as I can see, the Suggests dependencies of a package are not included in the docker containers. Would you consider adding these? It would be nice to be able to run all examples and vignette code of the packages available in a container.

From the README file, I understand that rake devel_base should use the in files in src/base and create the corresponding files in out/base. This fails however when I don't have anything already present in out. For example, when experimenting with an mscore image, I get

...
building devel_mscore from Dockerfile in out/devel_mscore...
...

and I can reproduce this if I remove any of the src directories for the existing images. What am I missing?

The release proteomics fails to build as does the devel_proteomics. From the tags it doesn't look like we have had a working image since Bioc 3.8. If the docker image is not updated to build successful we will be removing it as a listed available docker image after the next release.

Hi, in https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/devel_mscore2/builds/d7a4ddb7-52ab-494a-b572-e88142c3d283
we get

installing to /usr/local/lib/R/site-library/00LOCK-ChemmineOB/00new/ChemmineOB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::DoubleType"’: no definition for class “_p_OpenBabel::DoubleType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)

There are no no definition for class on http://bioconductor.org/checkResults/3.8/bioc-LATEST/ChemmineR/malbec1-install.html

There is a build error:

** testing if installed package can be loaded
Error: package or namespace load failed for ‘mzR’ 
in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/mzR/libs/mzR.so': /usr/local/lib/R/site-library/mzR/libs/mzR.so: 
undefined symbol: _ZNK2H58CommonFG15getObjnameByIdxB5cxx11Ey

in
https://hub.docker.com/r/bioconductor/devel_mscore2/builds/b5m6spuitr4cbpvbx4envjr/

This is the reason for the failure of devel_protmetcore2:

Warning: unable to access index for repository 
https://bioconductor.org/packages/3.6/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/PACKAGES'
Warning: dependencies ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’, ‘GO.db’, ‘hgu133plus2.db’, ‘hgu133a.db’, ‘KEGG.db’ are not available

and indeed, I get a 404 for https://bioconductor.org/packages/3.6/data/annotation/src/contrib/PACKAGES
while the same works for 3.5. I thing devel_protmetcore2 will fix itself once this works again.

Yours,
Steffen

Hi, the image currently doesn't due to a BiGGR error:

http://bioconductor.org/checkResults/devel/bioc-LATEST/BiGGR/malbec2-install.html

** byte-compile and prepare package for lazy loading
Error: object ‘species’ is not exported by 'namespace:rsbml'
Execution halted

Hi,

Installing package(s) 'ChemmineOB'

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/ChemmineOB_1.21.0.tar.gz'
Content type 'application/x-gzip' length 1185822 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... no
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -I/usr/include/eigen3  -DUSE_BOOST -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp:745:31: fatal error: openbabel/generic.h: No such file or directory
 #include <openbabel/generic.h>
                               ^
compilation terminated.

We need to add the openbabel header and lib location during the build,
see bioconductor.org/packages/devel/bioc/install/ChemmineOB/INSTALL
Yours, Steffen

Tracking the issues with the proteomics2 container, I identified the following issue when running

biocLite("Cairo")

gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -I. -Iinclude  -I/usr/local/include  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xlib-backend.c -o xlib-backend.o
xlib-backend.c:34:74: fatal error: X11/Intrinsic.h: No such file or directory
 #include <X11/Intrinsic.h>      /*->    Xlib.h  Xutil.h Xresource.h .. */
                                                                          ^
compilation terminated.
/usr/local/lib/R/etc/Makeconf:159: recipe for target 'xlib-backend.o' failed
make: *** [xlib-backend.o] Error 1
ERROR: compilation failed for package ‘Cairo’
* removing ‘/usr/local/lib/R/site-library/Cairo’

The downloaded source packages are in
	‘/tmp/Rtmp1hA2tS/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Cairo’ had non-zero exit status

I think that adding libx11-dev to the list of apt-get install packages will fix this.

Any suggestions whether it would be best to add in a lower-level container such as base?

The current bioconductor image seems to have a mismatch between the R version (3.2.0) and Bioconductor (3.0).

I pulled the latest bioconductor image from docker registry and used the following dockerfile to build an image with additional packages installed:

FROM bioconductor/release_core:latest

RUN Rscript -e "BiocInstaller::biocLite('limma')"

The output shows the following warnings:

Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
Warning message:
BiocInstaller version 3.0 is too old for R version 3.2.0;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R") 

The image does build, but the bioconductor version it contains seems out of date (should be 3.1).

I'm trying to build and push the devel_core image to my docker hub but rake isn't working for me. I have used docker login and edited my auth.yml file. This is the error I'm getting:

> rake devel_core
running task devel_base...
rake aborted!
LoadError: cannot load such file -- docker
/home/user/Documents/github/bioc_docker/Rakefile:26:in `setup_docker'
/home/user/Documents/github/bioc_docker/Rakefile:66:in `block (3 levels) in <top (required)>'
Tasks: TOP => devel_core => devel_base
(See full trace by running task with --trace)

rake, version 10.5.0
Docker version 1.12.5, build 7392c3b

Thanks, MR

Hi, just as a reminder, only the first 50 packages are installed,
@lgatto can you check about the rest ? Yours, Steffen

https://github.com/Bioconductor/bioc_docker/blob/master/out/devel_proteomics/install.R#L42

## test - there are 96 packages
## installing 48 works
## works with 65, R3.4.0_Bioc3.5 only though
pkgs_to_install <- pkgs_to_install[1:50]

I just tried rerunning after the merged pull request - It appears the devel_metabolomics2 was cancelled most likely reaching the time limit. Here is the log file:
https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/devel_metabolomics2/hub-builddetail/bwd2ydt7yvmtdr72fpl6p8m

I see this when working with the current devel_core2 container:

R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 

https://hub.docker.com/r/bioconductor/release_protmetcore2/builds/bqcyh3r5s3dsfqfwqjbvpew/

1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘ChemmineR’ had non-zero exit status 
2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘bioassayR’ had non-zero exit status

ChemmineR fails because of library(gridExtra) : there is no package called ‘gridExtra’

Hi, it would be great to document the build system setup,
i.e. to use rake to create the actual Dockerfiles in out/*

Several of these dockerfiles are overriding the R_LIBS_USER variable by forcing it to '' in the .Renviron file:

This causes a problem in that the R_LIBS_USER variable is suppressed. So, users using the container and expecting to be able to add a user-specific library cannot do so.

Is there a suggested way to use these images with R_LIBS_USER? If not, I suggest not overriding this value, because there is no way for the user to undo this and get the default functionality back.

Hi, it seems that devel_metabolomics2 is killed due to build time quota.
https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/

Most reasonable solution might be to inspect packages,
and manually select a subset, and add another container
possibly called devel_metabolomics_all covering the remaining
packages in the MetabolomicsView. Yours, Steffen

I added a new protcore container as an intermediate before building all proteomics packages, as the later always times out.

@lshep - could you add it to the docker hub, or tell me how to do it. Thanks!

Steffen,

After wiping the system again and then installinr r-base by "sudo apt-get install r-base", then following the instructions here: https://github.com/Bioconductor/bioc_docker/blob/master/out/release_protmetcore/Dockerfile, I got an error at "install.R/tmp", "No such directory". I procedded to try and install both xcms alone or just mzR, which seems to be the problem. The log for the mzR installation is below.

``
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

source("http://bioconductor.org/biocLite.R") # downloads the latest bioconductor script/repos
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most
recent version of R; see http://bioconductor.org/install

biocLite("mzR")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘mzR’
--2017-05-04 11:02:26-- https://bioconductor.org/packages/3.2/bioc/src/contrib/mzR_2.4.1.tar.gz
Resolving bioconductor.org (bioconductor.org)... 52.84.0.54, 52.84.0.118, 52.84.0.10, ...
Connecting to bioconductor.org (bioconductor.org)|52.84.0.54|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 14656607 (14M) [application/x-gzip]
Saving to: ‘/tmp/Rtmpskg3Y4/downloaded_packages/mzR_2.4.1.tar.gz’

 0K .......... .......... .......... .......... ..........  0% 1.77M 8s
50K .......... .......... .......... .......... ..........  0% 3.31M 6s

100K .......... .......... .......... .......... .......... 1% 3.28M 5s
150K .......... .......... .......... .......... .......... 1% 3.23M 5s
200K .......... .......... .......... .......... .......... 1% 3.28M 5s
250K .......... .......... .......... .......... .......... 2% 3.25M 5s
300K .......... .......... .......... .......... .......... 2% 3.26M 5s
350K .......... .......... .......... .......... .......... 2% 2.49M 5s
400K .......... .......... .......... .......... .......... 3% 3.28M 5s
450K .......... .......... .......... .......... .......... 3% 3.31M 5s
500K .......... .......... .......... .......... .......... 3% 3.29M 5s
550K .......... .......... .......... .......... .......... 4% 3.33M 4s
600K .......... .......... .......... .......... .......... 4% 3.26M 4s
650K .......... .......... .......... .......... .......... 4% 3.25M 4s
700K .......... .......... .......... .......... .......... 5% 3.27M 4s
750K .......... .......... .......... .......... .......... 5% 2.46M 4s
800K .......... .......... .......... .......... .......... 5% 3.30M 4s
850K .......... .......... .......... .......... .......... 6% 3.29M 4s
900K .......... .......... .......... .......... .......... 6% 3.27M 4s
950K .......... .......... .......... .......... .......... 6% 3.23M 4s
1000K .......... .......... .......... .......... .......... 7% 3.32M 4s
1050K .......... .......... .......... .......... .......... 7% 3.22M 4s
1100K .......... .......... .......... .......... .......... 8% 3.23M 4s
1150K .......... .......... .......... .......... .......... 8% 2.44M 4s
1200K .......... .......... .......... .......... .......... 8% 3.26M 4s
1250K .......... .......... .......... .......... .......... 9% 3.25M 4s
1300K .......... .......... .......... .......... .......... 9% 3.28M 4s
1350K .......... .......... .......... .......... .......... 9% 3.23M 4s
1400K .......... .......... .......... .......... .......... 10% 3.24M 4s
1450K .......... .......... .......... .......... .......... 10% 3.26M 4s
1500K .......... .......... .......... .......... .......... 10% 3.31M 4s
1550K .......... .......... .......... .......... .......... 11% 2.47M 4s
1600K .......... .......... .......... .......... .......... 11% 3.26M 4s
1650K .......... .......... .......... .......... .......... 11% 3.26M 4s
1700K .......... .......... .......... .......... .......... 12% 3.22M 4s
1750K .......... .......... .......... .......... .......... 12% 3.28M 4s
1800K .......... .......... .......... .......... .......... 12% 3.33M 4s
1850K .......... .......... .......... .......... .......... 13% 3.46M 4s
1900K .......... .......... .......... .......... .......... 13% 3.30M 4s
1950K .......... .......... .......... .......... .......... 13% 2.47M 4s
2000K .......... .......... .......... .......... .......... 14% 3.31M 4s
2050K .......... .......... .......... .......... .......... 14% 3.33M 4s
2100K .......... .......... .......... .......... .......... 15% 3.25M 4s
2150K .......... .......... .......... .......... .......... 15% 3.31M 4s
2200K .......... .......... .......... .......... .......... 15% 3.29M 4s
2250K .......... .......... .......... .......... .......... 16% 3.25M 4s
2300K .......... .......... .......... .......... .......... 16% 3.21M 4s
2350K .......... .......... .......... .......... .......... 16% 2.45M 4s
2400K .......... .......... .......... .......... .......... 17% 3.20M 4s
2450K .......... .......... .......... .......... .......... 17% 3.25M 4s
2500K .......... .......... .......... .......... .......... 17% 3.24M 4s
2550K .......... .......... .......... .......... .......... 18% 3.25M 4s
2600K .......... .......... .......... .......... .......... 18% 3.29M 4s
2650K .......... .......... .......... .......... .......... 18% 3.22M 4s
2700K .......... .......... .......... .......... .......... 19% 3.21M 4s
2750K .......... .......... .......... .......... .......... 19% 2.40M 4s
2800K .......... .......... .......... .......... .......... 19% 3.30M 4s
2850K .......... .......... .......... .......... .......... 20% 3.26M 4s
2900K .......... .......... .......... .......... .......... 20% 3.24M 4s
2950K .......... .......... .......... .......... .......... 20% 3.20M 4s
3000K .......... .......... .......... .......... .......... 21% 3.23M 4s
3050K .......... .......... .......... .......... .......... 21% 3.26M 4s
3100K .......... .......... .......... .......... .......... 22% 3.28M 4s
3150K .......... .......... .......... .......... .......... 22% 2.38M 4s
3200K .......... .......... .......... .......... .......... 22% 3.23M 3s
3250K .......... .......... .......... .......... .......... 23% 3.29M 3s
3300K .......... .......... .......... .......... .......... 23% 3.25M 3s
3350K .......... .......... .......... .......... .......... 23% 3.22M 3s
3400K .......... .......... .......... .......... .......... 24% 3.20M 3s
3450K .......... .......... .......... .......... .......... 24% 3.27M 3s
3500K .......... .......... .......... .......... .......... 24% 3.26M 3s
3550K .......... .......... .......... .......... .......... 25% 2.47M 3s
3600K .......... .......... .......... .......... .......... 25% 3.21M 3s
3650K .......... .......... .......... .......... .......... 25% 3.22M 3s
3700K .......... .......... .......... .......... .......... 26% 3.26M 3s
3750K .......... .......... .......... .......... .......... 26% 3.22M 3s
3800K .......... .......... .......... .......... .......... 26% 3.29M 3s
3850K .......... .......... .......... .......... .......... 27% 3.22M 3s
3900K .......... .......... .......... .......... .......... 27% 3.25M 3s
3950K .......... .......... .......... .......... .......... 27% 2.45M 3s
4000K .......... .......... .......... .......... .......... 28% 3.24M 3s
4050K .......... .......... .......... .......... .......... 28% 3.27M 3s
4100K .......... .......... .......... .......... .......... 28% 3.22M 3s
4150K .......... .......... .......... .......... .......... 29% 3.23M 3s
4200K .......... .......... .......... .......... .......... 29% 3.17M 3s
4250K .......... .......... .......... .......... .......... 30% 3.19M 3s
4300K .......... .......... .......... .......... .......... 30% 3.19M 3s
4350K .......... .......... .......... .......... .......... 30% 2.40M 3s
4400K .......... .......... .......... .......... .......... 31% 3.23M 3s
4450K .......... .......... .......... .......... .......... 31% 3.25M 3s
4500K .......... .......... .......... .......... .......... 31% 3.23M 3s
4550K .......... .......... .......... .......... .......... 32% 3.21M 3s
4600K .......... .......... .......... .......... .......... 32% 3.20M 3s
4650K .......... .......... .......... .......... .......... 32% 3.23M 3s
4700K .......... .......... .......... .......... .......... 33% 3.23M 3s
4750K .......... .......... .......... .......... .......... 33% 2.46M 3s
4800K .......... .......... .......... .......... .......... 33% 3.27M 3s
4850K .......... .......... .......... .......... .......... 34% 3.22M 3s
4900K .......... .......... .......... .......... .......... 34% 3.23M 3s
4950K .......... .......... .......... .......... .......... 34% 3.24M 3s
5000K .......... .......... .......... .......... .......... 35% 3.26M 3s
5050K .......... .......... .......... .......... .......... 35% 3.23M 3s
5100K .......... .......... .......... .......... .......... 35% 3.23M 3s
5150K .......... .......... .......... .......... .......... 36% 2.53M 3s
5200K .......... .......... .......... .......... .......... 36% 3.21M 3s
5250K .......... .......... .......... .......... .......... 37% 3.24M 3s
5300K .......... .......... .......... .......... .......... 37% 3.21M 3s
5350K .......... .......... .......... .......... .......... 37% 3.19M 3s
5400K .......... .......... .......... .......... .......... 38% 3.16M 3s
5450K .......... .......... .......... .......... .......... 38% 3.17M 3s
5500K .......... .......... .......... .......... .......... 38% 3.19M 3s
5550K .......... .......... .......... .......... .......... 39% 2.36M 3s
5600K .......... .......... .......... .......... .......... 39% 3.25M 3s
5650K .......... .......... .......... .......... .......... 39% 3.25M 3s
5700K .......... .......... .......... .......... .......... 40% 3.23M 3s
5750K .......... .......... .......... .......... .......... 40% 3.20M 3s
5800K .......... .......... .......... .......... .......... 40% 3.19M 3s
5850K .......... .......... .......... .......... .......... 41% 3.13M 3s
5900K .......... .......... .......... .......... .......... 41% 3.16M 3s
5950K .......... .......... .......... .......... .......... 41% 2.45M 3s
6000K .......... .......... .......... .......... .......... 42% 3.23M 3s
6050K .......... .......... .......... .......... .......... 42% 3.19M 3s
6100K .......... .......... .......... .......... .......... 42% 3.22M 3s
6150K .......... .......... .......... .......... .......... 43% 3.18M 3s
6200K .......... .......... .......... .......... .......... 43% 3.24M 3s
6250K .......... .......... .......... .......... .......... 44% 3.23M 3s
6300K .......... .......... .......... .......... .......... 44% 3.23M 3s
6350K .......... .......... .......... .......... .......... 44% 2.36M 2s
6400K .......... .......... .......... .......... .......... 45% 3.21M 2s
6450K .......... .......... .......... .......... .......... 45% 3.26M 2s
6500K .......... .......... .......... .......... .......... 45% 3.23M 2s
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6600K .......... .......... .......... .......... .......... 46% 3.23M 2s
6650K .......... .......... .......... .......... .......... 46% 3.20M 2s
6700K .......... .......... .......... .......... .......... 47% 3.24M 2s
6750K .......... .......... .......... .......... .......... 47% 2.47M 2s
6800K .......... .......... .......... .......... .......... 47% 3.29M 2s
6850K .......... .......... .......... .......... .......... 48% 3.22M 2s
6900K .......... .......... .......... .......... .......... 48% 3.17M 2s
6950K .......... .......... .......... .......... .......... 48% 3.21M 2s
7000K .......... .......... .......... .......... .......... 49% 3.14M 2s
7050K .......... .......... .......... .......... .......... 49% 3.28M 2s
7100K .......... .......... .......... .......... .......... 49% 3.30M 2s
7150K .......... .......... .......... .......... .......... 50% 2.48M 2s
7200K .......... .......... .......... .......... .......... 50% 3.32M 2s
7250K .......... .......... .......... .......... .......... 51% 3.20M 2s
7300K .......... .......... .......... .......... .......... 51% 3.23M 2s
7350K .......... .......... .......... .......... .......... 51% 3.25M 2s
7400K .......... .......... .......... .......... .......... 52% 3.26M 2s
7450K .......... .......... .......... .......... .......... 52% 3.32M 2s
7500K .......... .......... .......... .......... .......... 52% 3.31M 2s
7550K .......... .......... .......... .......... .......... 53% 2.41M 2s
7600K .......... .......... .......... .......... .......... 53% 3.19M 2s
7650K .......... .......... .......... .......... .......... 53% 3.24M 2s
7700K .......... .......... .......... .......... .......... 54% 3.27M 2s
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7850K .......... .......... .......... .......... .......... 55% 3.23M 2s
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7950K .......... .......... .......... .......... .......... 55% 2.45M 2s
8000K .......... .......... .......... .......... .......... 56% 3.24M 2s
8050K .......... .......... .......... .......... .......... 56% 3.29M 2s
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8150K .......... .......... .......... .......... .......... 57% 3.20M 2s
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8350K .......... .......... .......... .......... .......... 58% 2.48M 2s
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9200K .......... .......... .......... .......... .......... 64% 3.31M 2s
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10000K .......... .......... .......... .......... .......... 70% 3.19M 1s
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11150K .......... .......... .......... .......... .......... 78% 2.46M 1s
11200K .......... .......... .......... .......... .......... 78% 3.32M 1s
11250K .......... .......... .......... .......... .......... 78% 3.25M 1s
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11350K .......... .......... .......... .......... .......... 79% 3.18M 1s
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11450K .......... .......... .......... .......... .......... 80% 3.24M 1s
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11550K .......... .......... .......... .......... .......... 81% 2.48M 1s
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11800K .......... .......... .......... .......... .......... 82% 3.27M 1s
11850K .......... .......... .......... .......... .......... 83% 3.26M 1s
11900K .......... .......... .......... .......... .......... 83% 3.26M 1s
11950K .......... .......... .......... .......... .......... 83% 2.41M 1s
12000K .......... .......... .......... .......... .......... 84% 3.25M 1s
12050K .......... .......... .......... .......... .......... 84% 3.29M 1s
12100K .......... .......... .......... .......... .......... 84% 3.31M 1s
12150K .......... .......... .......... .......... .......... 85% 3.25M 1s
12200K .......... .......... .......... .......... .......... 85% 3.28M 1s
12250K .......... .......... .......... .......... .......... 85% 3.25M 1s
12300K .......... .......... .......... .......... .......... 86% 3.28M 1s
12350K .......... .......... .......... .......... .......... 86% 2.47M 1s
12400K .......... .......... .......... .......... .......... 86% 3.29M 1s
12450K .......... .......... .......... .......... .......... 87% 3.28M 1s
12500K .......... .......... .......... .......... .......... 87% 3.26M 1s
12550K .......... .......... .......... .......... .......... 88% 3.24M 1s
12600K .......... .......... .......... .......... .......... 88% 3.26M 1s
12650K .......... .......... .......... .......... .......... 88% 3.25M 1s
12700K .......... .......... .......... .......... .......... 89% 3.29M 0s
12750K .......... .......... .......... .......... .......... 89% 2.47M 0s
12800K .......... .......... .......... .......... .......... 89% 3.27M 0s
12850K .......... .......... .......... .......... .......... 90% 3.23M 0s
12900K .......... .......... .......... .......... .......... 90% 3.27M 0s
12950K .......... .......... .......... .......... .......... 90% 3.16M 0s
13000K .......... .......... .......... .......... .......... 91% 3.24M 0s
13050K .......... .......... .......... .......... .......... 91% 3.24M 0s
13100K .......... .......... .......... .......... .......... 91% 3.22M 0s
13150K .......... .......... .......... .......... .......... 92% 2.44M 0s
13200K .......... .......... .......... .......... .......... 92% 3.21M 0s
13250K .......... .......... .......... .......... .......... 92% 3.29M 0s
13300K .......... .......... .......... .......... .......... 93% 3.24M 0s
13350K .......... .......... .......... .......... .......... 93% 3.24M 0s
13400K .......... .......... .......... .......... .......... 93% 3.23M 0s
13450K .......... .......... .......... .......... .......... 94% 3.25M 0s
13500K .......... .......... .......... .......... .......... 94% 3.26M 0s
13550K .......... .......... .......... .......... .......... 95% 2.45M 0s
13600K .......... .......... .......... .......... .......... 95% 3.23M 0s
13650K .......... .......... .......... .......... .......... 95% 3.24M 0s
13700K .......... .......... .......... .......... .......... 96% 3.25M 0s
13750K .......... .......... .......... .......... .......... 96% 3.24M 0s
13800K .......... .......... .......... .......... .......... 96% 3.29M 0s
13850K .......... .......... .......... .......... .......... 97% 3.27M 0s
13900K .......... .......... .......... .......... .......... 97% 3.21M 0s
13950K .......... .......... .......... .......... .......... 97% 2.40M 0s
14000K .......... .......... .......... .......... .......... 98% 3.24M 0s
14050K .......... .......... .......... .......... .......... 98% 3.30M 0s
14100K .......... .......... .......... .......... .......... 98% 3.26M 0s
14150K .......... .......... .......... .......... .......... 99% 3.24M 0s
14200K .......... .......... .......... .......... .......... 99% 3.22M 0s
14250K .......... .......... .......... .......... .......... 99% 3.18M 0s
14300K .......... ... 100% 4.59M=4.5s

2017-05-04 11:02:31 (3.11 MB/s) - ‘/tmp/Rtmpskg3Y4/downloaded_packages/mzR_2.4.1.tar.gz’ saved [14656607/14656607]

• installing source package ‘mzR’ ...
  ** libs
  rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/Version.o ./pwiz...
  find . -name *~ -exec rm {} ; ## from cleanup
  find . -name *.o -exec rm {} ; ## from cleanup
  find . -name "#*#" -exec rm {} ; ## from cleanup
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cramp.cpp -o cramp.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ramp_base64.cpp -o ramp_base64.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ramp.cpp -o ramp.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppRamp.cpp -o RcppRamp.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppRampModule.cpp -o RcppRampModule.o
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnetCDF.c -o rnetCDF.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o
  In file included from ./boost/format/alt_sstream.hpp:20:0,
  from ./boost/format/internals.hpp:23,
  from ./boost/format.hpp:38,
  from ./pwiz/utility/misc/String.hpp:30,
  from pwiz/utility/misc/Std.hpp:31,
  from RcppPwiz.h:19,
  from RcppPwiz.cpp:1:
  ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename ...T>
  ^
  ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename T, typename U, typename ...U2>
  ^
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwizModule.cpp -o RcppPwizModule.o
  In file included from ./boost/format/alt_sstream.hpp:20:0,
  from ./boost/format/internals.hpp:23,
  from ./boost/format.hpp:38,
  from ./pwiz/utility/misc/String.hpp:30,
  from pwiz/utility/misc/Std.hpp:31,
  from RcppPwiz.h:19,
  from RcppPwizModule.cpp:2:
  ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename ...T>
  ^
  ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename T, typename U, typename ...U2>
  ^
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppIdent.cpp -o RcppIdent.o
  In file included from ./boost/format/alt_sstream.hpp:20:0,
  from ./boost/format/internals.hpp:23,
  from ./boost/format.hpp:38,
  from ./pwiz/utility/misc/String.hpp:30,
  from pwiz/utility/misc/Std.hpp:31,
  from RcppIdent.h:14,
  from RcppIdent.cpp:1:
  ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename ...T>
  ^
  ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename T, typename U, typename ...U2>
  ^
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppIdentModule.cpp -o RcppIdentModule.o
  In file included from ./boost/format/alt_sstream.hpp:20:0,
  from ./boost/format/internals.hpp:23,
  from ./boost/format.hpp:38,
  from ./pwiz/utility/misc/String.hpp:30,
  from pwiz/utility/misc/Std.hpp:31,
  from RcppIdent.h:14,
  from RcppIdentModule.cpp:2:
  ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename ...T>
  ^
  ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename T, typename U, typename ...U2>
  ^
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
  In file included from ./boost/thread/pthread/once_atomic.hpp:17:0,
  from ./boost/thread/once.hpp:20,
  from boost/thread/src/pthread/./once_atomic.cpp:9,
  from boost/thread/src/pthread/once.cpp:8:
  ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class Fp, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  ^
  In file included from ./boost/thread/once.hpp:20:0,
  from boost/thread/src/pthread/./once_atomic.cpp:9,
  from boost/thread/src/pthread/once.cpp:8:
  ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename Function, class ...ArgTypes>
  ^
  ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  ^
  g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/thread.cpp -o boost/thread/src/pthread/thread.o
  In file included from ./boost/chrono/duration.hpp:42:0,
  from ./boost/chrono/time_point.hpp:33,
  from ./boost/thread/lock_types.hpp:22,
  from ./boost/thread/pthread/thread_data.hpp:12,
  from ./boost/thread/thread_only.hpp:17,
  from boost/thread/src/pthread/thread.cpp:11:
  ./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename... T>
  ^
  ./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename T, typename U, typename... V>
  ^
  In file included from ./boost/thread/detail/thread.hpp:21:0,
  from ./boost/thread/thread_only.hpp:22,
  from boost/thread/src/pthread/thread.cpp:11:
  ./boost/thread/detail/make_tuple_indices.hpp:35:26: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template std::size_t... struct tuple_indices
  ^
  ./boost/thread/detail/make_tuple_indices.hpp:41:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <std::size_t Sp, std::size_t ...Indices, std::size_t Ep>
  ^
  ./boost/thread/detail/make_tuple_indices.hpp:47:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <std::size_t Ep, std::size_t ...Indices>
  ^
  In file included from ./boost/thread/detail/thread.hpp:22:0,
  from ./boost/thread/thread_only.hpp:22,
  from boost/thread/src/pthread/thread.cpp:11:
  ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class A, class A0, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class Fp, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template <class Ret, class ...Args>
  ^
  ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  ^
  ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  ^
  In file included from ./boost/thread/once.hpp:20:0,
  from boost/thread/src/pthread/thread.cpp:17:
  ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  template<typename Function, class ...ArgTypes>
  ^
  ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  ^
  boost/thread/src/pthread/thread.cpp: In function ‘boost::detail::thread_data_base boost::detail::get_current_thread_data()’:
  boost/thread/src/pthread/thread.cpp:140:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  In file included from ./boost/thread/once.hpp:20:0,
  from boost/thread/src/pthread/thread.cpp:17:
  ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t, boost::detail::thread_move_t...)
  inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  ^
  ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
  boost/thread/src/pthread/thread.cpp:140:88: note: mismatched types ‘boost::detail::thread_move_t’ and ‘void ()()’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  In file included from boost/thread/src/pthread/thread.cpp:17:0:
  ./boost/thread/once.hpp:35:13: note: candidate: template void boost::call_once(Function, boost::once_flag&)
  inline void call_once(Function func,once_flag& flag)
  ^
  ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
  boost/thread/src/pthread/thread.cpp:140:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  boost/thread/src/pthread/thread.cpp: In function ‘void boost::detail::set_current_thread_data(boost::detail::thread_data_base)’:
  boost/thread/src/pthread/thread.cpp:146:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  In file included from ./boost/thread/once.hpp:20:0,
  from boost/thread/src/pthread/thread.cpp:17:
  ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t, boost::detail::thread_move_t...)
  inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  ^
  ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
  boost/thread/src/pthread/thread.cpp:146:88: note: mismatched types ‘boost::detail::thread_move_t’ and ‘void ()()’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  In file included from boost/thread/src/pthread/thread.cpp:17:0:
  ./boost/thread/once.hpp:35:13: note: candidate: template void boost::call_once(Function, boost::once_flag&)
  inline void call_once(Function func,once_flag& flag)
  ^
  ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
  boost/thread/src/pthread/thread.cpp:146:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’
  boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  ^
  /usr/lib/R/etc/Makeconf:143: recipe for target 'boost/thread/src/pthread/thread.o' failed
  make: *** [boost/thread/src/pthread/thread.o] Error 1
  ERROR: compilation failed for package ‘mzR’
• removing ‘/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/mzR’

The downloaded source packages are in
‘/tmp/Rtmpskg3Y4/downloaded_packages’
Old packages: 'boot', 'cluster', 'codetools', 'foreign', 'lattice',
'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'
Update all/some/none? [a/s/n]:

Hi,
https://hub.docker.com/r/bioconductor/devel_protmetcore2/builds/bsqsbgg4l89fy5jr889yyfh/
seems to build alright, but then fails to push. Time limit ? Image Size limit ?

Successfully built 59e43fd9f16a 
Successfully tagged bioconductor/devel_protmetcore2:latest 
Pushing index.docker.io/bioconductor/devel_protmetcore2:latest... 
Build canceled.

Yours, Steffen

I will submit PR shortly. Let me what else I need to do in order for it to appear in https://hub.docker.com/r/bioconductor

The latest mscore built successfully, and proteomics is currently being re-built - fingers crossed. I haven't managed to do a good job at testing my changes locally because proteomics depends on mscore that is fetched from the docker hub. Here is a description

1. I identify that I need to add libx11-dev to the failing container for an R package to build. Adding this new apt-get dependency to proteomics allows me to build the container locally.
2. But I would prefer that dependency to be added to the parent container mscore. I make the change there and build it successfully locally.
3. How can I test proteomics so that it uses the locally built mscore (step 2) rather then fetch bioconductor/proteomics from docker hub.

Without being able to test step 3, I need to wait that the containers get updated remotely before being sure that the child container effectively builds/works.

@lshep @sneumann - Any idea how to address my question in step 3?

Package http://bioconductor.org/checkResults/devel/bioc-LATEST/mQTL.NMR/
has to be disabled since it causes failure:
https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/bsmjp3nbsmy2hmufp5pjsde/

due to missing dependency https://cran.r-project.org/web/packages/GenABEL/index.html

Package ‘GenABEL’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
Archived on 2018-05-25 as check problems were not corrected despite reminders. 

Yours, Steffen

I'm trying to install Bioconductor's DESeq2 via a docker container, and based on a Biostars suggestion, I went with the following Dockerfile setup:

Dockerfile

FROM bioconductor/release_base2

# Helps clean up Docker images
RUN rm -rf /var/lib/apt/lists/*

ADD setup.R /tmp/

# invalidates cache every 24 hours
ADD http://master.bioconductor.org/todays-date /tmp/

RUN R -f /tmp/setup.R

setup.R

pkgs <- c(
    "IRanges",
    "GenomicRanges",
    "ggplot2",
    "dplyr",
    "optparse",
    "SummarizedExperiment",
    "S4Vectors"
    )

ap.db <- available.packages(contrib.url(BiocManager::repositories()))
ap <- rownames(ap.db)
fnd <- pkgs %in% ap
pkgs_to_install <- pkgs[fnd]

ok <- BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE) %in% rownames(installed.packages())

if (!all(fnd))
    message("Packages not found in a valid repository (skipped):\n  ",
            paste(pkgs[!fnd], collapse="  \n  "))
if (!all(ok))
    stop("Failed to install:\n  ",
         paste(pkgs_to_install[!ok], collapse="  \n  "))

suppressWarnings(BiocManager::install(update=TRUE, ask=FALSE))

When I try to run this container interactively though, I get this response:

sudo docker run -v /home/ec2-user/data/:/data -it 096401932500.dkr.ecr.us-west-2.amazonaws.com/deseq2:dev
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] add: executing... 
Nothing additional to add
[cont-init.d] add: exited 0.
[cont-init.d] userconf: executing... 


ERROR: You must set a unique PASSWORD (not 'rstudio') first! e.g. run with:
docker run -e PASSWORD=<YOUR_PASS> -p 8787:8787 rocker/rstudio

Is there a better approach? Also, I want to be able to install python packages within the dockerfile (as I will be running this container on a python-based pipeline) - how can I properly conduct a multi-stage build to do so? I tried doing the following for this, but then my invoked python script run_deseq2.py responded with: /bin/sh: 1: Rscript: not found:

FROM bioconductor/release_base2

ADD src/setup.R /
RUN Rscript /setup.R 

ENV PATH=/usr/local/bin/:$PATH

FROM ubuntu:19.04 
 
ENV DEBIAN_FRONTEND=noninteractive  
 
WORKDIR / 
 
RUN apt-get update && \ 
    apt-get install -y \ 
        python-dev \ 
        python-pip \ 
        wget 
 
RUN pip install awscli boto3

COPY src/run_deseq2.py /
COPY src/s3_utils.py /
COPY src/job_utils.py /
COPY src/deseq2.R /
COPY src/ModelLoxTag.R /

ENV PATH=$PATH:~/.local/bin/ 
ENV R_THREADS=30 

# Run docker, starting with run script
ENTRYPOINT ["python", "/run_deseq2.py"]

I have rebuilt the base and core devel (R3.6.0 Bioc 3.9) and release (Bioc3.8 R 3.5.1) images. The devel_mscore2 image is failing. Because this image is failing none of the other devel containers can be built. Please look into this.

Things are getting a bit weird with the proteomics container. I am documenting my progress (or lack thereof here), and may be someone can chime in.

Currently, both release and devel fail. But I get release to build locally:

But devel fails

I believe that these fail should be fixed with the addition of libxt-dev in mscore, but...

On release, it is present, which is consistent with the positive result above

On devel, it is *not present, which is consistent with the negative result above

Not sure why ...

This line

vcontainer_name = version_name + "_" + container_name

creates a vcontainer variable that is never used. Not sure if it's a superfluous v or something else is going on.

Just wanted to point out that deleting temporary files in a Dockerfile doesn't reduce image size — unless you delete them in the same RUN that created them.

This is because each RUN command builds a separate image layer. After a layer has been built, any files that it added to the image are "baked in" and will contribute to final image size even if you delete them in a subsequent layer. In such a case, the deletion only serves to make files inaccessible in the running container.

The solution is to execute downloads/installs and cleanups in the same RUN, so only the net result gets baked into the image. Files that were added then removed in the same RUN are completely excluded from the single resulting layer.

RUN curl https://example.com/example.tar.gz | tar xz -C temp \
 && apt-get update \
 && apt-get install -y some-app \
 && some-app temp \
 && apt-get remove -y some-app \
 && apt-get clean \
 && rm -rf temp

As discussed by email, @sneumann will maintain metabolomics images and I will for proteomics images, and we will push to this repository. How is it for the docker hub? Are these pushed/tested automatically as part of the Bioconductor account?

Should we then user our own accounts for any images that are not (yet) under the Bioconductor hub?

Hi,
the last builds of devel_metabolomics2 are killed during the automated builds.
https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/bpstlewv4gnnrvyeclryhn8/
Reason is that linking ddalpha.so consumes large (>=6 GB) of RAM,
and the hub.docker build machines probably have a limit set.

...
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ddalpha.so AlphaProcedure.o Common.o DKnn.o HD.o Knn.o Mahalanobis.o OjaDepth.o Polynomial.o PotentialDepth.o ProjectionDepth.o SimplicialDepth.o TukeyDepth.o ZonoidDepth.o asa047.o ddalpha.o depth.fd.o init.o stdafx.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR �[91minstalling to /usr/local/lib/R/site-library/ddalpha/libs
byte-compile and prepare package for lazy loading
Killed

Locally the devel_metabolomics2 builds just fine.

Ideas ?

Yours, Steffen