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This page was generated on 2025-01-23 12:12 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 1657/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.30.0  (landing page)
Andrey A Shabalin
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/ramwas
git_branch: RELEASE_3_20
git_last_commit: 3a1566e
git_last_commit_date: 2024-10-29 10:16:10 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ramwas on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ramwas
Version: 1.30.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ramwas_1.30.0.tar.gz
StartedAt: 2025-01-21 10:07:07 -0000 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 10:11:42 -0000 (Tue, 21 Jan 2025)
EllapsedTime: 274.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ramwas_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ramwas.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ramwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ramwas’ version ‘1.30.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 code 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 7.713  0.227   7.957
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ramwas.Rcheck/00check.log’
for details.


Installation output

ramwas.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ramwas
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘ramwas’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c rw_c_code.c -o rw_c_code.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/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)

Tests output


Example timings

ramwas.Rcheck/ramwas-Ex.timings

nameusersystemelapsed
MakeBED000
QCs0.0350.0040.039
cachedRDSload1.4410.0001.448
findBestNpvs0.0020.0000.001
get0.0010.0000.000
getCpGset4.2130.0924.530
injectSNPsMAF0.8540.0000.856
insilicoFASTQ0.0010.0000.001
isAbsolutePath000
makefullpath000
manhattan7.7130.2277.957
mat2cols0.0010.0000.001
orthonormalizeCovariates0.0100.0000.009
parameterDump0.0030.0000.003
parameterPreprocess0.0010.0070.007
parametersFromFile0.0020.0000.001
pipeline0.0010.0000.000
plotCV2.1190.0202.141
plotFragmentSizeDistributionEstimate0.030.000.03
plotPC0.0110.0000.012
processCommandLine0.0010.0000.001
pvalue2qvalue0.0010.0000.000
qqplotFast1.6620.0481.713
ramwas0createArtificialData0.1990.0040.204
ramwasAnnotateLocations0.0000.0000.001
ramwasParameters000
rowcolSumSq0.0000.0000.001
rwDataClass-class0.0160.0000.016
subsetData000
testPhenotype0.0160.0040.019