lconway Summary
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| Package: DMEA |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMEA |
| BuildTime: 1 minutes 59.58 seconds |
| CheckCommand: BiocCheckGitClone('DMEA') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3015/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3015/430f5d49248ce3a9be84a332141ccc8602121ede/DMEA.install-out.txt DMEA_0.99.1.tar.gz && BiocCheck('DMEA_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 28.38 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DMEA_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 5.44 seconds |
| PackageFileSize: 235.67 KiB |
| BuildID:: DMEA_20230614204735 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DMEA. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘DMEA/DESCRIPTION’ ... OK
* preparing ‘DMEA’:
* 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 ‘DMEA_0.99.1.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('DMEA')
===============================
─ BiocCheckVersion: 1.37.2
─ BiocVersion: 3.18
─ Package: DMEA
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3015/430f5d49248ce3a9be84a332141ccc8602121ede/DMEA
─ 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...
* Checking that provided CITATION file is correctly formatted...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
It is recommended to use ‘given’ instead of ‘middle’.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3015/430f5d49248ce3a9be84a332141ccc8602121ede/DMEA.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMEA’ 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 serialization versions ... OK
* checking whether package ‘DMEA’ 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 R 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 ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... [6s/7s] 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 files in ‘vignettes’ ... OK
* checking examples ... [7s/108s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DMEA 1.614 0.709 45.701
drugSEA 1.043 0.496 32.022
rank_corr 0.323 0.221 14.663
as_gmt 0.154 0.202 13.240
* 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 ... [6s/7s] OK
* DONE
Status: OK
===============================
BiocCheck('DMEA_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.2
─ BiocVersion: 3.18
─ Package: DMEA
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXMb0J8/file31516c03cbc5/DMEA
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXMb0J8/file315140a0b803
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3015/430f5d49248ce3a9be84a332141ccc8602121ede/DMEA.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...
* 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...
* 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...
* NOTE: License 'CC0' unknown; licenses cannot restrict 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 DMEA...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 7 functions greater than 50 lines.
* Checking man page documentation...
* 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; 10 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 889 lines
(41%) 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 ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the DMEA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DMEA_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘DMEA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DMEA)
nebbiolo2 Summary
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| Package: DMEA |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DMEA |
| BuildTime: 0 minutes 6.91 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: DMEA_20230614204735 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DMEA. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘DMEA/DESCRIPTION’ ... OK
* preparing ‘DMEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DMEA.Rmd’ using rmarkdown
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 71
slots that were requested by the application:
/home/biocbuild/bbs-3.18-bioc/R/bin/Rscript
Either request fewer slots for your application, or make more slots
available for use.
A "slot" is the Open MPI term for an allocatable unit where we can
launch a process. The number of slots available are defined by the
environment in which Open MPI processes are run:
1. Hostfile, via "slots=N" clauses (N defaults to number of
processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the
hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an
RM is present, Open MPI defaults to the number of processor cores
In all the above cases, if you want Open MPI to default to the number
of hardware threads instead of the number of processor cores, use the
--use-hwthread-cpus option.
Alternatively, you can use the --oversubscribe option to ignore the
number of available slots when deciding the number of processes to
launch.
--------------------------------------------------------------------------
Quitting from lines 96-99 [unnamed-chunk-5] (DMEA.Rmd)
Error: processing vignette 'DMEA.Rmd' failed with diagnostics:
MPI_ERR_SPAWN: could not spawn processes
--- failed re-building ‘DMEA.Rmd’
SUMMARY: processing the following file failed:
‘DMEA.Rmd’
Error: Vignette re-building failed.
Execution halted
nebbiolo2 CHECK output
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nebbiolo2 BUILD BIN output
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