| Back to Build/check report for BioC 3.17 |
|
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 ramwas package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ramwas.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 1578/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ramwas 1.23.0 (landing page) Andrey A Shabalin
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: ramwas |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ramwas_1.23.0.tar.gz |
| StartedAt: 2023-02-07 12:42:05 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 12:51:56 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 591.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ramwas.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ramwas_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ramwas.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 ‘ramwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ramwas’ version ‘1.23.0’
* 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 ‘ramwas’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... OK
* 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 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
manhattan 9.723 0.472 10.2
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘RW1_intro.Rmd’... OK
‘RW2_CpG_sets.Rmd’... OK
‘RW3_BAM_QCs.Rmd’... OK
‘RW4_SNPs.Rmd’... OK
‘RW5a_matrix.Rmd’... OK
‘RW5c_matrix.Rmd’... OK
‘RW6_param.Rmd’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘RW1_intro.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotACbD-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotFSD-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotPCA-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotPCA-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotPCA-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/tableMWAS-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotCV1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW1_intro_files/figure-html/plotCV2-1.png" but not available.
--- finished re-building ‘RW1_intro.Rmd’
--- re-building ‘RW2_CpG_sets.Rmd’ using rmarkdown
--- finished re-building ‘RW2_CpG_sets.Rmd’
--- re-building ‘RW3_BAM_QCs.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW3_BAM_QCs_files/figure-html/hist.score1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW3_BAM_QCs_files/figure-html/hist.length.matched-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW3_BAM_QCs_files/figure-html/hist.edit.dist1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW3_BAM_QCs_files/figure-html/avg.coverage.by.density-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW3_BAM_QCs_files/figure-html/hist.isolated.dist1-1.png" but not available.
--- finished re-building ‘RW3_BAM_QCs.Rmd’
--- re-building ‘RW4_SNPs.Rmd’ using rmarkdown
Killed
--- re-building ‘RW5a_matrix.Rmd’ using rmarkdown
--- finished re-building ‘RW5a_matrix.Rmd’
--- re-building ‘RW5c_matrix.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/plotPCA-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/plotPCA-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/plotPCA-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/plotPCA-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/plotPCA-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/vign_test/ramwas/vignettes/RW5c_matrix_files/figure-html/tableMWAS-1.png" but not available.
--- finished re-building ‘RW5c_matrix.Rmd’
--- re-building ‘RW6_param.Rmd’ using rmarkdown
--- finished re-building ‘RW6_param.Rmd’
SUMMARY: processing the following file failed:
‘RW4_SNPs.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/ramwas.Rcheck/00check.log’
for details.
ramwas.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ramwas ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ramwas’ ... ** 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 rw_c_code.c -o rw_c_code.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ramwas/00new/ramwas/libs ** R ** 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 ** 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 (ramwas)
ramwas.Rcheck/ramwas-Ex.timings
| name | user | system | elapsed | |
| MakeBED | 0 | 0 | 0 | |
| QCs | 0.032 | 0.005 | 0.038 | |
| cachedRDSload | 1.520 | 0.000 | 1.521 | |
| findBestNpvs | 0.002 | 0.000 | 0.001 | |
| get | 0 | 0 | 0 | |
| getCpGset | 4.335 | 0.088 | 4.446 | |
| injectSNPsMAF | 0.909 | 0.004 | 0.914 | |
| insilicoFASTQ | 0.001 | 0.000 | 0.001 | |
| isAbsolutePath | 0.001 | 0.000 | 0.001 | |
| makefullpath | 0.001 | 0.000 | 0.001 | |
| manhattan | 9.723 | 0.472 | 10.200 | |
| mat2cols | 0.001 | 0.000 | 0.001 | |
| orthonormalizeCovariates | 0.009 | 0.000 | 0.009 | |
| parameterDump | 0.002 | 0.000 | 0.003 | |
| parameterPreprocess | 0.006 | 0.002 | 0.011 | |
| parametersFromFile | 0.000 | 0.001 | 0.001 | |
| pipeline | 0.000 | 0.001 | 0.001 | |
| plotCV | 2.006 | 0.037 | 2.044 | |
| plotFragmentSizeDistributionEstimate | 0.029 | 0.000 | 0.030 | |
| plotPC | 0.010 | 0.000 | 0.012 | |
| processCommandLine | 0.001 | 0.000 | 0.001 | |
| pvalue2qvalue | 0.000 | 0.000 | 0.001 | |
| qqplotFast | 2.079 | 0.104 | 2.184 | |
| ramwas0createArtificialData | 0.198 | 0.016 | 0.218 | |
| ramwasAnnotateLocations | 0 | 0 | 0 | |
| ramwasParameters | 0 | 0 | 0 | |
| rowcolSumSq | 0.000 | 0.001 | 0.001 | |
| rwDataClass-class | 0.012 | 0.002 | 0.014 | |
| subsetData | 0 | 0 | 0 | |
| testPhenotype | 0.018 | 0.000 | 0.018 | |