===============================
BiocCheckGitClone('protlocassign')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git
tracked:protlocassign.Rproj
protlocassign.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
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R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2541/protlocassign_20220309133537/protlocassign.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘protlocassign/DESCRIPTION’ ... OK
* this is package ‘protlocassign’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘protlocassign’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/6s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('protlocassign_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2541/protlocassign_20220309133537/protlocassign_0.99.1.tar.gz" "/tmp/Rtmph1WZAS/file353189442ac696/lib" 2>/dev/null' had status 1
* 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 for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 6.32 MB
Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
RNASeq
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 License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of protlocassign...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/cpaProgs.R (line 245, column 9)
cat() in R/cpaProgs.R (line 317, column 13)
cat() in R/cpaProgs.R (line 395, column 9)
print() in R/cpaProgs.R (line 32, column 9)
print() in R/cpaProgs.R (line 34, column 9)
print() in R/cpaProgs.R (line 36, column 9)
print() in R/cpaProgs.R (line 38, column 9)
print() in R/cpaProgs.R (line 42, column 9)
print() in R/cpaProgs.R (line 47, column 9)
print() in R/cpaProgs.R (line 65, column 9)
print() in R/cpaProgs.R (line 473, column 17)
print() in R/cpaProgs.R (line 475, column 17)
cat() in R/fCPAsubsets.r (line 43, column 9)
cat() in R/markerProfilePlot.r (line 47, column 9)
cat() in R/mixturePlotPanel.r (line 32, column 23)
cat() in R/profileSummarize.r (line 151, column 17)
cat() in R/profileSummarize.r (line 275, column 9)
cat() in R/profileSummarize.r (line 280, column 9)
cat() in R/protDistanceCompute.R (line 29, column 9)
cat() in R/proteinMix.r (line 36, column 9)
cat() in R/protPepProfilePlot.R (line 46, column 7)
cat() in R/protPepProfilePlot.R (line 51, column 5)
cat() in R/protProfilePlot.R (line 73, column 7)
cat() in R/protProfilePlot.R (line 78, column 5)
cat() in R/protProfilePlot.R (line 129, column 5)
cat() in R/RSAtransform.r (line 33, column 9)
cat() in R/RSAtransform.r (line 76, column 9)
cat() in R/RSAtransform.r (line 126, column 9)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 13 functions > 50 lines.
The longest 5 functions are:
protPlotfun() (R/protProfilePlot.R, line 40): 246 lines
protPepPlotfun() (R/protPepProfilePlot.R, line 31): 202 lines
mixturePlotPanel() (R/mixturePlotPanel.r, line 20): 164 lines
meansByProteins() (R/profileSummarize.r, line 52): 158 lines
fCPAone() (R/cpaProgs.R, line 281): 141 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
mixtureHeatMap.Rd, mixturePlotPanel.Rd, protPepPlotfun.Rd
* Checking package NEWS...
* 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; 239 lines (3%) are > 80 characters
long.
First 6 lines:
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:2 title: '...
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:13 %\Vig...
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:36 Determi...
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:38 This pa...
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:40 There a...
vignettes/vignette_1_protlocassign_introductory_tutorial.Rmd:42 We illu...
* NOTE: Consider multiples of 4 spaces for line indents, 1171
lines(15%) are not.
First 6 lines:
R/cpaProgs.R:84 # i=1
R/cpaProgs.R:85 loc.i <- location.list[i]
R/cpaProgs.R:87 # profile.i <-
R/cpaProgs.R:88 # meanReferenceProts[meanReferenceProts$reference...
R/cpaProgs.R:89 # == loc.i,2+1:numDataCols]
R/cpaProgs.R:90 profile.i <-
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...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.