Andrey A Shabalin
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/ramwas |
| git_branch: RELEASE_3_18 |
| git_last_commit: cb4c072 |
| git_last_commit_date: 2023-10-24 10:54:39 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:16 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1654/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ramwas 1.26.0 (landing page) Andrey A Shabalin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the ramwas package: - 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 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: ramwas |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ramwas_1.26.0.tar.gz |
| StartedAt: 2024-04-16 02:43:00 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:06:07 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1386.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ramwas.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ramwas_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ramwas.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ramwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ramwas’ version ‘1.26.0’
* 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 11.4.0-1ubuntu1~22.04) 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 ... 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 8.877 1.068 9.948
* 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’... failed
‘RW5c_matrix.Rmd’... OK
‘RW6_param.Rmd’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘RW5a_matrix.Rmd’
...
> download.file(url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE42861&format=file",
+ destfile = "GSE42861_RAW.tar", quiet = TRUE, mode .... [TRUNCATED]
Warning in download.file(url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE42861&format=file", :
downloaded length 0 != reported length 0
Warning in download.file(url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE42861&format=file", :
URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE42861&format=file': Timeout of 600 seconds was reached
When sourcing ‘RW5a_matrix.R’:
Error: download from 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE42861&format=file' failed
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ramwas.Rcheck/00check.log’
for details.
ramwas.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ramwas ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘ramwas’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-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 | 0.021 | 0.008 | 0.028 | |
| cachedRDSload | 1.723 | 0.340 | 2.062 | |
| findBestNpvs | 0.002 | 0.000 | 0.002 | |
| get | 0.001 | 0.000 | 0.000 | |
| getCpGset | 3.362 | 0.512 | 3.877 | |
| injectSNPsMAF | 0.785 | 0.024 | 0.809 | |
| insilicoFASTQ | 0.001 | 0.000 | 0.001 | |
| isAbsolutePath | 0.001 | 0.000 | 0.001 | |
| makefullpath | 0.000 | 0.000 | 0.001 | |
| manhattan | 8.877 | 1.068 | 9.948 | |
| mat2cols | 0.001 | 0.000 | 0.001 | |
| orthonormalizeCovariates | 0.007 | 0.000 | 0.007 | |
| parameterDump | 0.002 | 0.000 | 0.002 | |
| parameterPreprocess | 0.011 | 0.000 | 0.031 | |
| parametersFromFile | 0.000 | 0.002 | 0.001 | |
| pipeline | 0.000 | 0.001 | 0.001 | |
| plotCV | 1.870 | 0.036 | 1.906 | |
| plotFragmentSizeDistributionEstimate | 0.021 | 0.004 | 0.024 | |
| plotPC | 0.010 | 0.000 | 0.009 | |
| processCommandLine | 0.001 | 0.000 | 0.000 | |
| pvalue2qvalue | 0.001 | 0.000 | 0.000 | |
| qqplotFast | 0.664 | 0.148 | 0.813 | |
| ramwas0createArtificialData | 0.170 | 0.028 | 0.199 | |
| ramwasAnnotateLocations | 0 | 0 | 0 | |
| ramwasParameters | 0 | 0 | 0 | |
| rowcolSumSq | 0.001 | 0.000 | 0.001 | |
| rwDataClass-class | 0.012 | 0.000 | 0.012 | |
| subsetData | 0 | 0 | 0 | |
| testPhenotype | 0.017 | 0.000 | 0.016 | |