R CMD check rawR_0.1.1.tar.gz
* package encoding: UTF-8
* checking CRAN incoming feasibility ... ERROR
Maintainer: 'Christian Panse <[email protected]>'
New submission
Conflicting package names (submitted: rawR, existing: rawr [https://CRAN.R-project.org])
Conflicting package names (submitted: rawR, existing: rawr [CRAN archive])
The Title field should be in title case. Current version is:
'Access to Thermo Fisher Scientific raw files from R'
In title case that is:
R> BiocCheck("rawR_0.1.1.tar.gz")
This is BiocCheck version 1.26.0. BiocCheck is a work in
progress. Output and severity of issues may change. Installing
package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
Package version 0.1.1; pre-release
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'rawRcolor.tif'
* Checking biocViews...
* Checking that biocViews are present...
* ERROR: No biocViews terms found.
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball
name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import grDevices, graphics, utils in
DESCRIPTION as well as NAMESPACE.
* Checking vignette directory...
This is an unknown type of package
* ERROR: No 'vignettes' directory.
* Checking library calls...
* Checking for library/require of rawR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
rawR.R (line 1011, column 29)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
rawR.R (line 600, column 36)
rawR.R (line 745, column 70)
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpLJg2l6/filedebd713f5408/rawR/tests/testthat/test-header.R'
* WARNING: Avoid class() == or class() != ; use is() or
!is()
Found in files:
R/rawR.R (line 68)
* Checking parsed R code in R directory, examples,
vignettes...
* Checking function lengths..........
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
plot.rawRspectrum() (R/rawR.R, line 711): 108 lines
readChromatogram() (R/rawR.R, line 429): 105 lines
print.rawRspectrum() (R/rawR.R, line 839): 84 lines
readFileHeader() (R/rawR.R, line 106): 61 lines
validate_rawRspectrum() (R/rawR.R, line 635): 52 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following
man pages: man/plot.rawRchromatogram.Rd,
man/plot.rawRchromatogramSet.Rd,
man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd,
man/summary.rawRspectrum.Rd
man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd,
man/summary.rawRspectrum.Rd
* ERROR: At least 80% of man pages documenting exported
objects must have runnable examples. The following pages
do not:
new_rawRspectrum.Rd, plot.rawRchromatogramSet.Rd,
validate_rawRspectrum.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.
14% of man pages use one of these cases.
Found in the following files:
readChromatogram.Rd
readSpectrum.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
readChromatogram.Rd
readSpectrum.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news
will be included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R
source, and vignette source...
* NOTE: Consider shorter lines; 32 lines (2%) are > 80
characters long.
First 6 lines:
R/rawR.R:7 .writeRData <- function(rawfile, outputfile=paste0...
R/rawR.R:14 list(scanType=rv$scanType, mZ=rv$mZ, inte...
R/rawR.R:28 warning("Can not find Mono JIT co...
R/rawR.R:41 rvs <- system2(Sys.which('mono'), arg...
R/rawR.R:64 #' pathToRawFile <- file.path(path.package(packag...
R/rawR.R:154 e$info$`Instrument method` <- ba...
* NOTE: Consider 4 spaces instead of tabs; 5 lines (0%)
contain tabs.
First 5 lines:
R/zzz.R:5 if(interactive()){
R/zzz.R:6 version <- packageVersion('rawR')
R/zzz.R:7 packageStartupMessage("Package 'rawR' version ", ...
R/zzz.R:8 invisible()
R/zzz.R:9 }
* NOTE: Consider multiples of 4 spaces for line indents,
233 lines(14%) are not.
First 6 lines:
R/rawR.R:107 mono = if(Sys.info()['sysname'] %in% c("Darwi...
R/rawR.R:108 exe = system.file('exec/rawR.exe',package = '...
R/rawR.R:109 mono_path = "",
R/rawR.R:110 argv = "infoR",
R/rawR.R:111 system2_call = TRUE,
R/rawR.R:112 method = "thermo"){
See
http://bioconductor.org/developers/how-to/coding-style/
See styler package:
https://cran.r-project.org/package=styler as described
in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* ERROR: Package must be removed from CRAN.
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed
to the bioc-devel mailing list (requires admin
credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Summary:
ERROR count: 4
WARNING count: 4
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.12/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "No biocViews terms found."
[2] "No 'vignettes' directory."
[3] "At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not:"
[4] "Package must be removed from CRAN."
$warning
[1] "The following files are over 5MB in size: 'rawRcolor.tif'"
[2] "Import grDevices, graphics, utils in DESCRIPTION as well as NAMESPACE."
[3] " Avoid class() == or class() != ; use is() or !is()"
[4] "Add non-empty \\value sections to the following man pages: man/plot.rawRchromatogram.Rd, man/plot.rawRchromatogramSet.Rd, man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd, man/summary.rawRspectrum.Rd"
$note
[1] " Avoid sapply(); use vapply()"
[2] " Avoid 1:...; use seq_len() or seq_along()"
[3] "Recommended function length <= 50 lines."
[4] "Usage of dontrun{} / donttest{} found in man page examples."
[5] "Use donttest{} instead of dontrun{}."
[6] "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."
[7] "Consider shorter lines; 32 lines (2%) are > 80 characters long."
[8] "Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs."
[9] "Consider multiples of 4 spaces for line indents, 233 lines(14%) are not."
R>