===============================
R CMD BUILD
===============================
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘nipalsMCIA_0.99.1.tar.gz’
===============================
BiocCheckGitClone('nipalsMCIA')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: nipalsMCIA
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2914/9e5785f03ee8112de4743b408805c326cb280c3a/nipalsMCIA
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
R/.DS_Store
vignettes/.DS_Store
* 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...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2914/9e5785f03ee8112de4743b408805c326cb280c3a/nipalsMCIA.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘0.99.1’
* 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 ‘nipalsMCIA’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [23s/23s] OK
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/59s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nipals_multiblock 5.024 0.076 5.1
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/2914/9e5785f03ee8112de4743b408805c326cb280c3a/nipalsMCIA.Rcheck/00check.log’
for details.
===============================
BiocCheck('nipalsMCIA_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: nipalsMCIA
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpLkLdK9/file1aab352f6bc5f4/nipalsMCIA
─ installDir: /tmp/RtmpLkLdK9/file1aab3539a77c35
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2914/9e5785f03ee8112de4743b408805c326cb280c3a/nipalsMCIA.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 3.5.0 to 4.3.0.
* Checking package size...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'inst/doc/Vignette2.Single-Cell-Analysis.html'
* 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...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 nipalsMCIA...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 29 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...
* 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...
* NOTE: Consider shorter lines; 88 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 730 lines
(19%) 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 name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 2 WARNINGS | 8 NOTES
See the nipalsMCIA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘nipalsMCIA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: S3 method ‘.DollarNames.MultiAssayExperiment’ was declared in NAMESPACE but not found
Error: package or namespace load failed for ‘nipalsMCIA’ in namespaceExport(ns, exports):
undefined exports: experiments<-, sampleMap<-, ExperimentList, MatchedAssayExperiment, MultiAssayExperiment, MultiAssayExperimentToMAF, anyReplicated, experiments, exportClass, getWithColData, hasAssay, hasRowRanges, intersectColumns, intersectRows, listToMap, loadHDF5MultiAssayExperiment, longFormat, makeHitList, mapToList, mergeReplicates, prepMultiAssay, renameColname, renamePrimary, replicated, replicates, sampleMap, saveHDF5MultiAssayExperiment, subsetByAssay, subsetByColData, subsetByColumn, subsetByRow, upsetSamples, wideFormat
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpwVapiQ/Rinst932d574800a2/nipalsMCIA’
-----------------------------------
ERROR: package installation failed