===============================
R CMD BUILD
===============================
* checking for file smoppix/DESCRIPTION ... OK
* preparing smoppix:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: smoppix
* saving partial Rd database
* 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 smoppix_0.99.32.tar.gz
===============================
BiocCheckGitClone('smoppix')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix
BiocVersion: 3.21
Package: smoppix
PackageVersion: 0.99.32
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.2 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/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file smoppix/DESCRIPTION ... OK
* checking extension type ... Package
* this is package smoppix version 0.99.32
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 smoppix can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [27s/27s] NOTE
plotCells: no visible binding for global variable gene
plotCells: no visible binding for global variable cell
plotWf: no visible binding for global variable minP
plotWf: no visible binding for global variable maxP
plotWf: no visible binding for global variable Weight
Undefined global functions or variables:
Weight cell gene maxP minP
* checking Rd files ... [8s/8s] 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 ... [1s/1s] INFO
Note: found 4 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [126s/103s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotTopResults 10.214 2.507 9.449
getResults 5.977 4.793 6.955
fitLMMs 7.487 2.741 6.892
writeToXlsx 7.445 2.512 6.674
evalWeightFunction 4.109 3.802 5.472
estGradients 2.207 0.609 8.500
getPvaluesGradient 2.237 0.524 8.739
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [228s/185s]
[229s/185s] 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 ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('smoppix_0.99.32.tar.gz')
===============================
Installing smoppix
Package installed successfully
smoppix session metadata
sourceDir: /tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix
BiocVersion: 3.21
Package: smoppix
PackageVersion: 0.99.32
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/894403e87eac99b081809363c84819f81ffc78dd/smoppix.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix
installDir: /tmp/RtmphR2OZ9/file39ed2a7261775f
isTarBall: TRUE
platform: unix
Running BiocCheck on smoppix
* 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 4.5.0.
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* 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...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* Checking for library/require of smoppix...
* 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 16
functions greater than 50 lines.
The longest 5 functions are:
addWeightFunction() (R/addWeightFunction.R): 158 lines
...
plotCells() (R/plotCells.R): 122 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmphR2OZ9/file39ed2a55a7e843/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* 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; 356 lines (10%) are > 80 characters long.
First few lines:
R/addCell.R#L7 #' The length of the list must match the ...
...
vignettes/smoppixVignette.Rmd#L438 often indicates insufficient memory. Try
...
i NOTE: Consider multiples of 4 spaces for line indents; 195 lines (5%) are
not.
First few lines:
R/addCell.R#L92 stop("Cells already present in hyp ...
...
vignettes/smoppixVignette.Rmd#L440 ...
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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the smoppix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.