===============================
R CMD BUILD
===============================
* checking for file ‘postNet/DESCRIPTION’ ... OK
* preparing ‘postNet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* 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_0.99.8.tar.gz’
===============================
BiocCheckGitClone('postNet')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet
→ BiocVersion: 3.23
→ Package: postNet
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet.BiocCheck
→ BiocCheckVersion: 1.47.23
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* 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 v1.47.23 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-05 09:26:00 UTC
* using option ‘--no-vignettes’
* checking for file ‘postNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘postNet’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 40 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
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.3Mb
libs 2.2Mb
* 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 ... [18s/18s] OK
* checking Rd files ... [1s/1s] 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [273s/236s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
featureIntegration 50.660 2.339 30.157
goAnalysis 36.713 1.955 38.702
ptn_GO 32.282 1.045 33.330
rfPred 28.509 1.320 16.458
codonCalc 9.696 0.444 10.123
ptn_codonAnalysis 9.524 0.157 9.650
codonUsage 9.225 0.186 9.388
ptn_codonSelection 9.166 0.027 9.153
plotSignatures_ads 8.293 0.142 8.428
postNetStart 7.380 0.055 7.435
slopeFilt 5.673 0.061 5.734
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/25s]
[22s/25s] OK
* 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 ... [7s/7s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet.Rcheck/00check.log’
for details.
===============================
BiocCheck('postNet_0.99.8.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing postNet ──────────────────────────────────────────────────────────
✔ Package installed successfully
── postNet session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1Ogbd6/file18134642df926f/postNet
→ BiocVersion: 3.23
→ Package: postNet
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4086/8a267437a287f177ccf49be0295a5e0553b27f35/postNet.BiocCheck
→ BiocCheckVersion: 1.47.23
→ sourceDir: /tmp/Rtmp1Ogbd6/file18134642df926f/postNet
→ installDir: /tmp/Rtmp1Ogbd6/file18134675bfa580
→ 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 4.5.0 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 (26%).
* 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...
* 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...
* 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 31
functions greater than 50 lines.
The longest 5 functions are:
• codonUsage() (R/codonUsage.R): 1287 lines
• ...
• plotSignatures_ads() (R/plotSignatures_ads.R): 489 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• gageAnalysis.Rd
• ...
• ptn_motifSelection.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 24% of man
pages use at least one of these tags.
Found in files:
• contentMotifs.Rd
• ...
• ptn_motifSelection.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• contentMotifs.Rd
• ...
• ptn_motifSelection.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...
i NOTE: Consider shorter lines; 1127 lines (6%) are > 80 characters long.
First few lines:
• R/codonUsage.R#L53 "ftp://ftp.ncbi.nlm. ...
• ...
• vignettes/postNet.Rmd#L1634 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#L1439 # hsa-miR-101-3p.1 -0.509 -0.279 1 0.024 ...
i NOTE: Consider multiples of 4 spaces for line indents; 2375 lines (13%) are
not.
First few lines:
• R/complementaryFunctions.R#L1009 min_score ...
• ...
• vignettes/postNet.Rmd#L1588 pdfName = "ExampleSignatures" ...
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 v1.47.23 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the postNet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.