Hi,

It seems that contrary to what doc mentions , it is not possible to use path = raw(0)
So as to export image to raw vecotr rather than writing to file.

I see the following:

Found pkg-config! 
Found pkg-config cflags and/or libs for libtiff! 
Using PKG_CFLAGS= 
Using PKG_LIBS=-ltiff -lwebp -lzstd -ljpeg -lz -lm 
** finished configure for package 'ijtiff'
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c common.c -o common.o
In file included from common.c:1:
common.h:26:32: error: conflicting types for 'uint64_t'; have 'long long unsigned int'
   26 | typedef unsigned long long int uint64_t;
      |                                ^~~~~~~~
In file included from /usr/include/stdint.h:37,
                 from /usr/lib/gcc/x86_64-redhat-linux/11/include/stdint.h:9,
                 from /usr/include/tiffconf-64.h:13,
                 from /usr/include/tiffconf.h:9,
                 from /usr/include/tiff.h:28,
                 from common.h:5,
                 from common.c:1:
/usr/include/bits/stdint-uintn.h:27:20: note: previous declaration of 'uint64_t' with type 'uint64_t' {aka 'long unsigned int'}
   27 | typedef __uint64_t uint64_t;
      |                    ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:168: common.o] Error 1
ERROR: compilation failed for package 'ijtiff'

See the complete log here

Hi! I wanted to reuse the src/makefile.win and tools/winlibs.R in my package, but ran into a problem testing ijtiff itself.

install.packages("ijtiff", type = "source")

Using that command in Windows 10 64-bit, installation of ijtiff fails with missing file errors, like tiffio.h (i can post a full error log if it'd help).

Is this expected? The binary version installs perfectly fine.

Thanks!

Hi! Are there plans to incorporate the ability to write TIFF file with metadata?

Does it support merge more than 4 channel images.
It looks like CMYK + extra alpha channels?

Fields can go for graphics, which is base and bbmisc function can be included by hand.

libbz2 libtiff libwebp libzstd liblzma libjpeg zlib1g libdeflate

👋 @rorynolan! GitHub linguist classifies your repo as html. You could create a .gitattributesfile at the root cf https://github.com/jeroen/jsonlite/blob/a68e1d46e2ae6450cd46c12be0e32fd66d12a90c/.gitattributes#L1 :-) (only a suggestion!)

👋 again!

I've added a few repo topics see below

Feel free to edit ("r" and "rstats" might seem useless but popular R package repos actually use them so I've added them to all ropensci packages)!

👋 @rorynolan I saw there was an update of ijtiff on CRAN but no GitHub release yet. Reminding you about this as this will ensure the update is included in the next rOpenSci newsletter (see https://ropensci.org/blog/2021/04/16/latest-ropensci-news-digest/#new-versions for instance).

In case this is new to you: to do a GitHub release the easiest solution is running usethis::use_github_release() and to not forget to use usethis::use_release_issue()

I have some problems to install the last version of ijtiff package in ubuntu 22.04.1 version (R 4.2.2). I get the same error both in R in terminal or in Rstudio: /usr/bin/ld: cannot find -lwebp: No such file or directory
I don't find any help in internet about this error.

sudo apt-get install libtiff5-dev

in terminal. No problem during installation.

Then in R:
install.packages("ijtiff")

Installation du package dans ‘/usr/local/lib/R/site-library’
(car ‘lib’ n'est pas spécifié)
essai de l'URL 'https://cloud.r-project.org/src/contrib/ijtiff_2.2.9.tar.gz'
Content type 'application/x-gzip' length 2433782 bytes (2.3 MB)

downloaded 2.3 MB

• installing source package ‘ijtiff’ ...
  ** package ‘ijtiff’ correctement décompressé et sommes MD5 vérifiées
  ** using staged installation
  ** preparing to configure package 'ijtiff' ...
  Found pkg-config!
  Found pkg-config cflags and/or libs for libtiff!
  Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
  Using PKG_LIBS=-ltiff -lwebp -lzstd -llzma -ljpeg -ldeflate -lz -lm
  ** finished configure for package 'ijtiff'
  ** libs
  gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -ffile-prefix-map=/build/r-base-anRV6o/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c common.c -o common.o
  gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -ffile-prefix-map=/build/r-base-anRV6o/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
  gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -ffile-prefix-map=/build/r-base-anRV6o/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read.c -o read.o
  gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -ffile-prefix-map=/build/r-base-anRV6o/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o
  gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -ffile-prefix-map=/build/r-base-anRV6o/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o
  gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o ijtiff.so common.o init.o read.o utils.o write.o -ltiff -lwebp -lzstd -llzma -ljpeg -ldeflate -lz -lm -L/usr/lib/R/lib -lR
  /usr/bin/ld: cannot find -lwebp: No such file or directory
  collect2: error: ld returned 1 exit status
  make: *** [/usr/share/R/share/make/shlib.mk:10: ijtiff.so] Error 1
  ERROR: compilation failed for package ‘ijtiff’
• removing ‘/usr/local/lib/R/site-library/ijtiff’
• restoring previous ‘/usr/local/lib/R/site-library/ijtiff’

Les packages source téléchargés sont dans
‘/tmp/RtmpMuUequ/downloaded_packages’
Message d'avis :
Dans install.packages("ijtiff") :
l'installation du package ‘ijtiff’ a eu un statut de sortie non nul

#############
Same output with
devtools::install_github("ropensci/ijtiff")

#################

R.version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 2.2
year 2022
month 10
day 31
svn rev 83211
language R
version.string R version 4.2.2 (2022-10-31)
nickname Innocent and Trusting

############
Ubuntu 22.04.1
############

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 compiler_4.2.2 later_1.3.0 urlchecker_1.0.1
[5] prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 tools_4.2.2
[9] digest_0.6.30 pkgbuild_1.3.1 pkgload_1.3.1 memoise_2.0.1
[13] lifecycle_1.0.3 rlang_1.0.6 shiny_1.7.3 cli_3.4.1
[17] curl_4.3.3 fastmap_1.1.0 withr_2.5.0 stringr_1.4.1
[21] fs_1.5.2 htmlwidgets_1.5.4 devtools_2.4.5 rprojroot_2.0.3
[25] glue_1.6.2 R6_2.5.1 processx_3.8.0 sessioninfo_1.2.2
[29] callr_3.7.3 purrr_0.3.5 magrittr_2.0.3 ps_1.7.2
[33] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.3 usethis_2.1.6
[37] mime_0.12 xtable_1.8-4 httpuv_1.6.6 stringi_1.7.8
[41] miniUI_0.1.1.1 cachem_1.0.6 crayon_1.5.2

👋 @rorynolan!

As part of the consolidation of our guidance for package developers I've added a paragraph about system dependencies to https://ropensci.github.io/dev_guide/building.html#package-dependencies I see your package depends on libtiff.

Could you:

• check for it in the configure script and give a helpful error message if it cannot be found

• add the libtiff entry to sysreqsdb https://github.com/r-hub/sysreqsdb#sysreqs ?

Please ask me any question you might have! This part of the guide is brand-new, and sysreqsdb README was just updated, so they can certainly be improved. Thank you!

Hi,

This package is failing for me when installing on Redhat 7.5.

First attempt at installing told us to install libtiff-devel. See below.

install.packages("/data/software/r_packages/ijtiff_1.5.1.tar.gz", lib="/usr/lib64/R/library")
inferring 'repos = NULL' from 'pkgs'
* installing *source* package ‘ijtiff’ ...
** package ‘ijtiff’ successfully unpacked and MD5 sums checked
** using staged installation
Package libtiff-4 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libtiff-4.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libtiff-4' found
Using PKG_CFLAGS=
Using PKG_LIBS=-ltiff -ljpeg -lz
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libtiff-4 was not found. Try installing:
 * deb: libtiff-dev (Debian, Ubuntu, etc)
 * rpm: libtiff-devel (Fedora, EPEL)
 * brew: libtiff (OSX)
If libtiff-4 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libtiff-4.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘ijtiff’
* removing ‘/usr/lib64/R/library/ijtiff’
Warning message:
In install.packages("/data/software/r_packages/ijtiff_1.5.1.tar.gz",  :

Installed that fine and now getting the following error.

install.packages("/data/software/r_packages/ijtiff_1.5.1.tar.gz", lib="/usr/lib64/R/library")
inferring 'repos = NULL' from 'pkgs'
* installing *source* package ‘ijtiff’ ...
** package ‘ijtiff’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-ltiff -ljbig -ljpeg -lz
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RcppExports.cpp -o RcppExports.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c common.c -o common.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c read.c -o read.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c utils.cpp -o utils.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG  -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c write.c -o write.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o ijtiff.so RcppExports.o common.o read.o utils.o write.o -ltiff -ljbig -ljpeg -lz -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -ljbig
collect2: error: ld returned 1 exit status
make: *** [ijtiff.so] Error 1
ERROR: compilation failed for package ‘ijtiff’
* removing ‘/usr/lib64/R/library/ijtiff’
Warning message:
In install.packages("/data/software/r_packages/ijtiff_1.5.1.tar.gz",  :

The installation page says to install libtiff5-dev but not sure that package exists on Fedora/Redhat? Can only see libtiff-devel unless that is the same.

On Fedora Linux, try sudo yum install libtiff5-dev, or if that doesn’t work, try
sudo yum install libtiff4-dev.

Any advice on installing would be appreciated.

Thanks

ljtiff tests fails with dev waldo because it now (correctly) distinguishes between NaN and NA:

── Failure ('test-io.R:124:3'): Float (real-numbered) TIFF I/O works ───────────
as.vector(in_tif) (`actual`) not equal to as.vector(a2345) (`expected`).

  `actual[6:12]`: 42 86 94 NaN 20 4 38
`expected[6:12]`: 42 86 94  NA 20 4 38

I couldn't get your package to compile so I couldn't do a PR myself, but the fix should be straightforward.

Hello, i am having an issue with a particular set of images.

I constructed an array with 4 dimensions, holding 60x60 images, with 49 frames and 4 channels.

> dim(tiff.arrays[[1]])
[1] 60 60  4 49

When converting it to ijtiff i get:

> pic <- ijtiff::as_ijtiff_img(tiff.arrays[[1]])
> pic
60x60 pixel ijtiff_img with 4 channels and 49 frames.
Preview (top left of first channel of first frame):
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,] 6487 6300 6429 6260 6335 6209
[2,] 6232 6405 6502 6419 6427 6464
[3,] 6403 6326 6405 6398 6430 6463
[4,] 6391 6211 6385 6349 6300 6495
[5,] 6376 6298 6468 6267 6531 6413
[6,] 6451 6352 6179 6381 6320 6324
── TIFF tags ──────────
>

The image was made from an array so there are no tags. Is this a problem?

I guessed that so far so good, so i save the tiff to a file:

  ijtiff::write_tif(pic, path = paste0("trabajo_final/imagenes/",i, ".tif"), 
                    overwrite = T, msg = F, bits_per_sample = 16)

Then i dragged and dropped it into imagej and got an weirdness:

• A "EOF" Java exception message from imagej/fiji: java.io.EOFException
• 3 channels instead of four
• 39 frames instead of 49 frames
• And this:

The bioformats plugin, however, reads them just fine:

If I choose to export only three channels out of the 4 channels i have, there is no problem:

 pic <- ijtiff::as_ijtiff_img(tiff.arrays[[1]][,,1:3,])
 ijtiff::write_tif(pic, path = paste0("trabajo_final/imagenes/",i, ".tif"), 
                   overwrite = T, msg = F, bits_per_sample = 16)

I guess something is not right around RGB having 3 channels and my image having 4. Also that the number of frames is close to 3/4 of the original.

Do you know what might be going on?

Thanks!

Could you please make sure to git tag each CRAN release https://github.com/ropensci/ijtiff/tags - looks like you got v1, but didn't git tag your most recent CRAN release

And plop in associated NEWS items for that release - thanks! e.g., https://github.com/ropensci/taxize/releases/tag/v0.9.3

These two things make it easier for people to find the associated changes with each new version

Sometimes you don't need all of the images. Then, it would be nice to be able to select to read just the ones you want (for the sake of speed).