===============================
R CMD BUILD
===============================
* checking for file postNet/DESCRIPTION ... OK
* preparing postNet:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building postNet_0.99.2.tar.gz
===============================
BiocCheckGitClone('postNet')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet
BiocVersion: 3.23
Package: postNet
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
postNet.Rproj
vignettes/Figures/.DS_Store
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet/.git/objects/pack/pack-47b95cc131ceca58725a36efccb453b66d9bfa93.pack
/home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet/.git/objects/pack/pack-47b95cc131ceca58725a36efccb453b66d9bfa93.pack
/home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet/.git/objects/pack/pack-47b95cc131ceca58725a36efccb453b66d9bfa93.pack
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.47.16 results
1 ERRORS | 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file postNet/DESCRIPTION ... OK
* checking extension type ... Package
* this is package postNet version 0.99.2
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 41 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 postNet can be installed ... OK
* checking installed package size ... INFO
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.3Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [19s/19s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'goAnalysis.Rd':
[DOSE]{enrichResult-class}
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [320s/281s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
featureIntegration 51.974 2.744 30.831
goAnalysis 37.698 0.858 38.580
ptn_GO 32.997 0.513 33.513
rfPred 30.145 1.590 17.444
gageAnalysis 27.753 1.364 29.122
ptn_GAGE 24.952 0.887 25.841
ptn_codonAnalysis 10.180 0.157 10.308
ptn_codonSelection 10.182 0.008 10.148
codonCalc 10.021 0.147 10.152
codonUsage 9.559 0.184 9.713
postNetStart 7.991 0.075 8.068
plotFeaturesMap 5.194 0.131 5.326
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [9s/9s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+03B1)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+03B1)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+2212)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character 2 (U+2082)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+03B1)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 2 WARNINGs
See
/home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet.Rcheck/00check.log
for details.
===============================
BiocCheck('postNet_0.99.2.tar.gz')
===============================
Installing postNet
Package installed successfully
postNet session metadata
sourceDir: /tmp/RtmpT1dWjq/file3fb0fc33d25f45/postNet
BiocVersion: 3.23
Package: postNet
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/44d7f71a0159214e3022552b732e00aa1e19120f/postNet.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /tmp/RtmpT1dWjq/file3fb0fc33d25f45/postNet
installDir: /tmp/RtmpT1dWjq/file3fb0fc4e1170da
isTarBall: TRUE
platform: unix
Running BiocCheck on postNet
* 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...
i NOTE: Update R version dependency from 4.4.0 to 4.6.0
* Checking package size...
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (28%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Evaluate more vignette chunks.
i 56 out of 83 code chunks = 67% unevaluated
i 0 non-exec code chunk(s) (e.g., '```r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of postNet...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/codonUsage.R (line 52, column 40)
...
R/uorfAnalysis.R (line 66, column 16)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
codonCalc.R (line 55, column 13)
...
uorfAnalysis.R (line 81, column 15)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/codonUsage.R (line 463, column 9)
...
cat() in R/plotSignatures.R (line 38, column 5)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/codonUsage.R (line 434, column 15)
...
R/rfPred.R (line 35, column 11)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/qcchecks.R (line 524, column 10)
...
R/qcchecks.R (line 555, column 12)
i NOTE: Avoid system() ; use system2()
Found in files:
system() in R/postNetStart.R (line 144, column 5)
system() in R/postNetStart.R (line 190, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
The longest 5 functions are:
codonUsage() (R/codonUsage.R): 614 lines
...
plotSignatures() (R/plotSignatures.R): 208 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
goDotplot.Rd
...
slopeFilt.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 26% of man
pages use at least one of these tags.
Found in files:
contentMotifs.Rd
...
slopeFilt.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
contentMotifs.Rd
...
slopeFilt.Rd
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1820 lines (14%) are > 80 characters long.
First few lines:
R/codonCalc.R#L16 stop("Codon analysis is NULL in the ...
...
vignettes/postNet.Rmd#L1584 Xu S, Hu E, Cai Y, Xie Z, Luo X, Zhan L, ...
i NOTE: Consider 4 spaces instead of tabs; 25 lines (0%) contain tabs.
First few lines:
man/postNetData-class.Rd#L60 } ...
...
vignettes/postNet.Rmd#L1391 # hsa-miR-101-3p.1 -0.509 -0.279 1 0 ...
i NOTE: Consider multiples of 4 spaces for line indents; 5642 lines (43%) are
not.
First few lines:
R/codonCalc.R#L2 featsel, ...
...
vignettes/postNet.Rmd#L1536 pdfName = "ExampleSign ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.16 results
0 ERRORS | 1 WARNINGS | i 17 NOTES
i See the postNet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.