| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:39 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1618/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.50.0 (landing page) Hans-Ulrich Klein
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the R453Plus1Toolbox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R453Plus1Toolbox.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: R453Plus1Toolbox |
| Version: 1.50.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings R453Plus1Toolbox_1.50.0.tar.gz |
| StartedAt: 2023-10-16 00:11:57 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:19:07 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 429.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings R453Plus1Toolbox_1.50.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.50.0’
* 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 ‘R453Plus1Toolbox’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.annotateVariants_MapperSet: no visible binding for global variable
‘Hsapiens’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.getEnsemblInfo: no visible binding for global variable ‘cds_length’
.getEnsemblInfo: no visible binding for global variable
‘ensembl_transcript_id’
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
.plotVariants: no visible binding for global variable ‘mutation’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
annotateVariants,MapperSet-BSgenome: no visible binding for global
variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
variable ‘Hsapiens’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
detectBreakpoints,list: no visible binding for global variable
‘Hsapiens’
subset,AVASet: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse
cds_length ensembl_transcript_id mutation referenceSeqID
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mergeBreakpoints 4.815 0.197 5.016
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘vignette.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.
R453Plus1Toolbox.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL R453Plus1Toolbox
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:27:7: warning: variable ‘block_count’ set but not used [-Wunused-but-set-variable]
27 | int block_count;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R453Plus1Toolbox)
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings
| name | user | system | elapsed | |
| AVASet-class | 1.115 | 0.012 | 1.129 | |
| AVASet | 0.124 | 0.004 | 0.129 | |
| AnnotatedVariants-class | 0.001 | 0.000 | 0.001 | |
| MapperSet-class | 0.021 | 0.012 | 0.032 | |
| MapperSet | 0.001 | 0.003 | 0.005 | |
| SFFContainer-class | 0.001 | 0.001 | 0.001 | |
| SFFRead-class | 0.001 | 0.000 | 0.001 | |
| alignShortReads | 2.130 | 0.112 | 2.249 | |
| annotateVariants | 0.001 | 0.000 | 0.001 | |
| assayDataAmp | 0.004 | 0.000 | 0.004 | |
| ava2vcf | 0.209 | 0.000 | 0.209 | |
| avaSetExample | 0.011 | 0.000 | 0.011 | |
| avaSetFiltered | 0.018 | 0.000 | 0.018 | |
| avaSetFiltered_annot | 0.002 | 0.000 | 0.002 | |
| breakpoints | 0.004 | 0.000 | 0.004 | |
| calculateTiTv | 0.008 | 0.000 | 0.008 | |
| captureArray | 0.001 | 0.000 | 0.002 | |
| coverageOnTarget | 0.178 | 0.004 | 0.183 | |
| demultiplexReads | 0.063 | 0.011 | 0.076 | |
| detectBreakpoints | 0.573 | 0.088 | 0.661 | |
| fDataAmp | 0.015 | 0.000 | 0.015 | |
| featureDataAmp | 0.013 | 0.000 | 0.013 | |
| filterChimericReads | 2.267 | 0.044 | 2.311 | |
| genomeSequencerMIDs | 0.022 | 0.000 | 0.022 | |
| getAlignedReads | 0.056 | 0.000 | 0.057 | |
| getVariantPercentages | 0.021 | 0.004 | 0.025 | |
| htmlReport | 3.098 | 0.148 | 3.227 | |
| mapperSetExample | 0.002 | 0.003 | 0.005 | |
| mergeBreakpoints | 4.815 | 0.197 | 5.016 | |
| mutationInfo | 0.002 | 0.000 | 0.002 | |
| plotAmpliconCoverage | 0 | 0 | 0 | |
| plotChimericReads | 2.689 | 0.104 | 2.793 | |
| plotVariants | 0.003 | 0.000 | 0.003 | |
| plotVariationFrequency | 0.001 | 0.000 | 0.001 | |
| qualityReportSFF | 0 | 0 | 0 | |
| readSFF | 0.085 | 0.000 | 0.085 | |
| readsOnTarget | 0.045 | 0.000 | 0.045 | |
| referenceSequences | 0.006 | 0.000 | 0.006 | |
| regions | 0.002 | 0.000 | 0.002 | |
| removeLinker | 0.018 | 0.000 | 0.018 | |
| sequenceCaptureLinkers | 0.004 | 0.000 | 0.004 | |
| setVariantFilter | 0.036 | 0.000 | 0.036 | |
| variants | 0.002 | 0.000 | 0.002 | |
| writeSFF | 0.023 | 0.004 | 0.026 | |