Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:01 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for ramwas on merida1


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.

raw results

Package 1565/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.20.0  (landing page)
Andrey A Shabalin
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/ramwas
git_branch: RELEASE_3_15
git_last_commit: 2c1206f
git_last_commit_date: 2022-04-26 11:38:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: ramwas
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ramwas.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ramwas_1.20.0.tar.gz
StartedAt: 2022-06-24 07:18:36 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 07:25:09 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 393.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ramwas.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ramwas_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ramwas.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ramwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ramwas’ version ‘1.20.0’
* 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
* 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 10.665  0.692  11.389
getCpGset  5.219  0.253   5.500
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ramwas.Rcheck/00check.log’
for details.



Installation output

ramwas.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ramwas
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ramwas’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rw_c_code.c -o rw_c_code.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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
QCs0.0560.0040.062
cachedRDSload1.4320.0031.437
findBestNpvs0.0020.0000.002
get0.0000.0000.001
getCpGset5.2190.2535.500
injectSNPsMAF0.8530.0130.867
insilicoFASTQ0.0020.0000.002
isAbsolutePath0.0010.0010.001
makefullpath0.0000.0000.001
manhattan10.665 0.69211.389
mat2cols0.0010.0000.002
orthonormalizeCovariates0.0130.0000.013
parameterDump0.0040.0010.005
parameterPreprocess0.0070.0050.015
parametersFromFile0.0010.0000.001
pipeline0.0020.0000.001
plotCV2.6580.0392.706
plotFragmentSizeDistributionEstimate0.0480.0030.051
plotPC0.0140.0020.017
processCommandLine0.0020.0010.002
pvalue2qvalue0.0000.0000.001
qqplotFast1.9020.2362.144
ramwas0createArtificialData0.3440.0330.379
ramwasAnnotateLocations0.0010.0000.001
ramwasParameters0.0010.0000.000
rowcolSumSq0.0010.0000.001
rwDataClass-class0.0750.0010.077
subsetData0.0010.0010.000
testPhenotype0.0290.0020.030