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R CMD BUILD
===============================
* checking for file mspms/DESCRIPTION ... OK
* preparing mspms:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* building mspms_0.99.0.tar.gz
===============================
BiocCheckGitClone('mspms')
===============================
BiocCheckVersion: 1.41.3
BiocVersion: 3.20
Package: mspms
PackageVersion: 0.99.0
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.Rcheck
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file mspms/DESCRIPTION ... OK
* checking extension type ... Package
* this is package mspms version 0.99.0
* 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 mspms can be installed ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE
plot_cleavages_per_pos: no visible binding for global variable
condition
plot_volcano: no visible binding for global variable condition
Undefined global functions or variables:
condition
* 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [263s/263s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_all_icelogos 50.485 0.032 50.517
mspms_t_tests 49.828 0.028 49.856
log2fc_t_test 49.704 0.084 49.790
plot_volcano 49.536 0.036 49.572
mspms_anova 22.441 0.031 22.473
handle_outliers 16.439 0.120 16.559
log2fct_time 7.997 0.001 7.997
log2fct_condition 7.968 0.000 7.968
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [22s/22s]
[23s/22s] 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.Rcheck/00check.log
for details.
===============================
BiocCheck('mspms_0.99.0.tar.gz')
===============================
BiocCheckVersion: 1.41.3
BiocVersion: 3.20
Package: mspms
PackageVersion: 0.99.0
sourceDir: /tmp/RtmpaU4kuG/file35c4ad7bd6ab90/mspms
installDir: /tmp/RtmpaU4kuG/file35c4ad201ee01d
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3460/mspms_20240701143310/mspms.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* 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 4.4.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up of less
than 3 sentences. Provide a more detailed description of the
package.
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* 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...
Bioconductor dependencies found in Imports & Depends (9%).
* 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...
* Checking for library/require of mspms...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 10 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 43 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 732 lines
(24%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 9 NOTES
See the mspms.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
* checking for file mspms/DESCRIPTION ... OK
* preparing mspms:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building mspms_analysis.Rmd using rmarkdown
Quitting from lines 221-226 [unnamed-chunk-4] (mspms_analysis.Rmd)
Error: processing vignette 'mspms_analysis.Rmd' failed with diagnostics:
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so, 0x0006): Symbol not found: (_iconv)
Referenced from: '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/readxl/libs/readxl.so'
Expected in: '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib'
--- failed re-building mspms_analysis.Rmd
SUMMARY: processing the following file failed:
mspms_analysis.Rmd
Error: Vignette re-building failed.
Execution halted