Andrey A Shabalin
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ramwas |
| Branch: RELEASE_3_12 |
| Last Commit: b13659e |
| Last Changed Date: 2020-10-27 11:20:16 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:06 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ramwas package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1449/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ramwas 1.14.0 (landing page) Andrey A Shabalin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ramwas |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ramwas.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ramwas_1.14.0.tar.gz |
| StartedAt: 2021-05-06 05:58:41 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:05:13 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 391.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ramwas.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ramwas.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ramwas_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ramwas.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ramwas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ramwas' version '1.14.0'
* 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 whether package 'ramwas' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpaIef9I/R.INSTALL1a7445c632c1/ramwas/man/QCs.Rd:71: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpaIef9I/R.INSTALL1a7445c632c1/ramwas/man/qqplotFast.Rd:91: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ramwas.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ramwas/libs/i386/ramwas.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ramwas/libs/x64/ramwas.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
manhattan 9.06 0.58 9.64
getCpGset 4.96 0.25 5.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
manhattan 10.43 0.77 11.2
* 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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/ramwas.Rcheck/00check.log'
for details.
ramwas.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ramwas_1.14.0.tar.gz && rm -rf ramwas.buildbin-libdir && mkdir ramwas.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ramwas.buildbin-libdir ramwas_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ramwas_1.14.0.zip && rm ramwas_1.14.0.tar.gz ramwas_1.14.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 209k 100 209k 0 0 11.2M 0 --:--:-- --:--:-- --:--:-- 11.3M
install for i386
* installing *source* package 'ramwas' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rw_c_code.c -o rw_c_code.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ramwas.buildbin-libdir/00LOCK-ramwas/00new/ramwas/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ramwas'
finding HTML links ... done
MakeBED html
QCs html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpaIef9I/R.INSTALL1a7445c632c1/ramwas/man/QCs.Rd:71: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
RaMWAS html
cachedRDSload html
findBestNpvs html
get html
getCpGset html
injectSNPsMAF html
finding level-2 HTML links ... done
insilicoFASTQ html
isAbsolutePath html
makefullpath html
manhattan html
mat2cols html
orthonormalizeCovariates html
parameterDump html
parameterPreprocess html
parametersFromFile html
pipeline html
plotCV html
plotFragmentSizeDistributionEstimate html
plotPC html
processCommandLine html
pvalue2qvalue html
qqplotFast html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpaIef9I/R.INSTALL1a7445c632c1/ramwas/man/qqplotFast.Rd:91: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
ramwas0createArtificialData html
ramwasAnnotateLocations html
ramwasParameters html
rowcolSumSq html
rwDataClass-class html
subsetData html
testPhenotype html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'ramwas' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rw_c_code.c -o rw_c_code.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ramwas.buildbin-libdir/ramwas/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ramwas' as ramwas_1.14.0.zip
* DONE (ramwas)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ramwas' successfully unpacked and MD5 sums checked
|
ramwas.Rcheck/examples_i386/ramwas-Ex.timings
|
ramwas.Rcheck/examples_x64/ramwas-Ex.timings
|