Johannes Helmuth
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/normr |
| git_branch: RELEASE_3_13 |
| git_last_commit: f1d3f26 |
| git_last_commit_date: 2021-09-20 10:47:57 -0400 (Mon, 20 Sep 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the normr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/normr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1280/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| normr 1.18.1 (landing page) Johannes Helmuth
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: normr |
| Version: 1.18.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings normr_1.18.1.tar.gz |
| StartedAt: 2021-10-15 02:47:26 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:54:23 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 417.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: normr.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings normr_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'normr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'normr' version '1.18.1'
* 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 'normr' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 2.2Mb
libs 2.4Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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-3.13-bioc/meat/normr.Rcheck/00check.log'
for details.
normr.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/normr_1.18.1.tar.gz && rm -rf normr.buildbin-libdir && mkdir normr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=normr.buildbin-libdir normr_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL normr_1.18.1.zip && rm normr_1.18.1.tar.gz normr_1.18.1.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
7 2228k 7 164k 0 0 619k 0 0:00:03 --:--:-- 0:00:03 619k
100 2228k 100 2228k 0 0 1963k 0 0:00:01 0:00:01 --:--:-- 1965k
install for i386
* installing *source* package 'normr' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em.cpp -o em.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normr_init.c -o normr_init.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
Creating a new generic function for 'getClasses' in package 'normr'
** help
*** installing help indices
converting help for package 'normr'
finding HTML links ... done
NormRCountConfig-class html
NormRFit-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/normRFit.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/normrfit.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/NormRfit.html
normR-diffR html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/diffr.html
finding level-2 HTML links ... done
normR-enrichR html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/enrichr.html
normR-regimeR html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/regimer.html
normR html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/help/normr.html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'normr' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em.cpp -o em.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normr_init.c -o normr_init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/normr.buildbin-libdir/normr/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
* MD5 sums
packaged installation of 'normr' as normr_1.18.1.zip
* DONE (normr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'normr' successfully unpacked and MD5 sums checked
|
normr.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(normr)
Attaching package: 'normr'
The following object is masked from 'package:methods':
getClasses
Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
>
> test_check("normr")
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 3 | SKIP 2 | PASS 439 ]
>
> proc.time()
user system elapsed
54.25 2.28 56.51
|
normr.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(normr)
Attaching package: 'normr'
The following object is masked from 'package:methods':
getClasses
Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
>
> test_check("normr")
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 3 | SKIP 2 | PASS 439 ]
>
> proc.time()
user system elapsed
52.32 0.68 53.00
|
|
normr.Rcheck/examples_i386/normr-Ex.timings
|
normr.Rcheck/examples_x64/normr-Ex.timings
|