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R CMD BUILD
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* 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_0.99.3.tar.gz
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BiocCheckGitClone('postNet')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet
BiocVersion: 3.23
Package: postNet
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet/.git/objects/pack/pack-79c13e8e8e109735c12006bfb10d3109ffad9999.pack
/home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet/.git/objects/pack/pack-79c13e8e8e109735c12006bfb10d3109ffad9999.pack
/home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet/.git/objects/pack/pack-79c13e8e8e109735c12006bfb10d3109ffad9999.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
0 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/c588cca99c5afcd1cb73aef337f750e2dd8976e5/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 0.99.3
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [21s/21s] 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 ... [205s/180s] ERROR
Running examples in postNet-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ptn_GAGE
> ### Title: Accessor for the "GAGE" slot of a 'postNetData' object
> ### Aliases: ptn_GAGE
>
> ### ** Examples
>
> # load example data:
> data("postNetExample", package = "postNet")
> ptn <- postNetExample$ptn
>
> # Run GAGE:
> ptn <- gageAnalysis(ptn,
+ category = "CC")
Loading required package: org.Hs.eg.db
Failed with error: package AnnotationDbi required by org.Hs.eg.db could not be found
Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
(2026-01-15 r89304)
Warning: package(s) not installed when version(s) same as or greater than current; use
`force = TRUE` to re-install: 'org.Hs.eg.db'
Loading required package: org.Hs.eg.db
Failed with error: package AnnotationDbi required by org.Hs.eg.db could not be found
Error in gage::go.gsets(species = species, id.type = "EG") :
Fail to install/load gene annotation package org.Hs.eg.db!
Calls: gageAnalysis -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
featureIntegration 54.112 2.456 32.076
goAnalysis 41.238 0.935 42.178
gageAnalysis 31.612 1.692 33.307
codonCalc 11.738 0.810 12.534
codonUsage 10.818 0.235 11.022
postNetStart 8.176 0.084 8.259
plotFeaturesMap 5.737 0.147 5.884
* 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: 2 ERRORs, 2 WARNINGs
See
/home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet.Rcheck/00check.log
for details.
===============================
BiocCheck('postNet_0.99.3.tar.gz')
===============================
Installing postNet
Package installed successfully
postNet session metadata
sourceDir: /tmp/RtmpD1u4kB/file327714c976cc7/postNet
BiocVersion: 3.23
Package: postNet
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/c588cca99c5afcd1cb73aef337f750e2dd8976e5/postNet.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /tmp/RtmpD1u4kB/file327714c976cc7/postNet
installDir: /tmp/RtmpD1u4kB/file3277157970810
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.