| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:22 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the R453Plus1Toolbox package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1572/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R453Plus1Toolbox 1.49.0 (landing page) Hans-Ulrich Klein
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: R453Plus1Toolbox |
| Version: 1.49.0 |
| 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/library --timings R453Plus1Toolbox_1.49.0.tar.gz |
| StartedAt: 2023-02-07 12:36:49 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 12:45:49 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 540.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: NA |
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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/library --timings R453Plus1Toolbox_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.49.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
R 2.0Mb
extdata 2.8Mb
* 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 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 7.815 0.10 8.043
filterChimericReads 5.075 0.02 5.101
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘vignette.Rnw’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘vignette.Rnw’
...
TargetRegion NoLinker MinimumDistance Unique5PrimeStart
1 23 23 23 23
> bp = detectBreakpoints(filterReads, minClusterSize = 1)
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Removing soft-clipped bases ... done
Determining consensus breakpoints ... Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 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/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
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/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 | 0.225 | 0.004 | 0.232 | |
| AVASet | 0.169 | 0.004 | 0.173 | |
| AnnotatedVariants-class | 0.002 | 0.000 | 0.001 | |
| MapperSet-class | 0.028 | 0.000 | 0.028 | |
| MapperSet | 0.006 | 0.000 | 0.006 | |
| SFFContainer-class | 0.000 | 0.000 | 0.001 | |
| SFFRead-class | 0.001 | 0.000 | 0.000 | |
| alignShortReads | 2.412 | 0.004 | 2.428 | |
| annotateVariants | 0.001 | 0.000 | 0.001 | |
| assayDataAmp | 0.005 | 0.000 | 0.005 | |
| ava2vcf | 0.279 | 0.000 | 0.279 | |
| avaSetExample | 0.014 | 0.000 | 0.013 | |
| avaSetFiltered | 0.02 | 0.00 | 0.02 | |
| avaSetFiltered_annot | 0.000 | 0.002 | 0.002 | |
| breakpoints | 0.003 | 0.001 | 0.004 | |
| calculateTiTv | 0.01 | 0.00 | 0.01 | |
| captureArray | 0.002 | 0.000 | 0.001 | |
| coverageOnTarget | 0.234 | 0.000 | 0.238 | |
| demultiplexReads | 0.085 | 0.012 | 0.097 | |
| detectBreakpoints | 0.825 | 0.068 | 0.895 | |
| fDataAmp | 0.007 | 0.010 | 0.017 | |
| featureDataAmp | 0.012 | 0.004 | 0.016 | |
| filterChimericReads | 5.075 | 0.020 | 5.101 | |
| genomeSequencerMIDs | 0.029 | 0.000 | 0.029 | |
| getAlignedReads | 0.068 | 0.000 | 0.070 | |
| getVariantPercentages | 0.023 | 0.008 | 0.031 | |
| htmlReport | 2.901 | 0.044 | 2.926 | |
| mapperSetExample | 0.002 | 0.004 | 0.006 | |
| mergeBreakpoints | 7.815 | 0.100 | 8.043 | |
| mutationInfo | 0.003 | 0.000 | 0.002 | |
| plotAmpliconCoverage | 0 | 0 | 0 | |
| plotChimericReads | 2.794 | 0.004 | 2.799 | |
| plotVariants | 0.003 | 0.000 | 0.003 | |
| plotVariationFrequency | 0 | 0 | 0 | |
| qualityReportSFF | 0.000 | 0.000 | 0.001 | |
| readSFF | 0.109 | 0.004 | 0.115 | |
| readsOnTarget | 0.065 | 0.000 | 0.064 | |
| referenceSequences | 0.008 | 0.000 | 0.008 | |
| regions | 0.000 | 0.003 | 0.003 | |
| removeLinker | 0.024 | 0.000 | 0.025 | |
| sequenceCaptureLinkers | 0.006 | 0.000 | 0.006 | |
| setVariantFilter | 0.051 | 0.000 | 0.052 | |
| variants | 0.003 | 0.000 | 0.002 | |
| writeSFF | 0.037 | 0.000 | 0.036 | |