| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:55 -0400 (Sat, 13 Apr 2019).
| Package 1613/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| universalmotif 1.0.22 Benjamin Jean-Marie Tremblay
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: universalmotif |
| Version: 1.0.22 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings universalmotif_1.0.22.tar.gz |
| StartedAt: 2019-04-13 06:07:48 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:12:19 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 270.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: universalmotif.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings universalmotif_1.0.22.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'universalmotif/DESCRIPTION' ... OK
* this is package 'universalmotif' version '1.0.22'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'universalmotif' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.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 ... NOTE
Unexported object imported by a ':::' call: 'TFBSTools:::schneider_correction'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motif_tree: no visible binding for global variable 'group'
motif_tree: no visible binding for global variable 'icscore'
convert_motifs,universalmotif: no visible binding for global variable
'2'
Undefined global functions or variables:
2 group icscore
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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-3.8-bioc/R/library/universalmotif/libs/i386/universalmotif.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 or elapsed time > 5s
user system elapsed
convert_motifs 8.92 0.65 9.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
convert_motifs 8.46 0.36 8.81
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.Rcheck/00check.log'
for details.
universalmotif.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/universalmotif_1.0.22.tar.gz && rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=universalmotif.buildbin-libdir universalmotif_1.0.22.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL universalmotif_1.0.22.zip && rm universalmotif_1.0.22.tar.gz universalmotif_1.0.22.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 408k 100 408k 0 0 10.1M 0 --:--:-- --:--:-- --:--:-- 11.0M
install for i386
* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c add_multifreq_helper.cpp -o add_multifreq_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c motif_simil_helper.cpp -o motif_simil_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c scan_sequences_helper.cpp -o scan_sequences_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c trim_motifs_helper.cpp -o trim_motifs_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c universalmotif_helper.cpp -o universalmotif_helper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o trim_motifs_helper.o universalmotif_helper.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.dll; fi
[[: not found
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.buildbin-libdir/universalmotif/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'convert_motifs' with signature 'motifs="MotifList"': no definition for class "MotifList"
in method for 'convert_motifs' with signature 'motifs="TFFMFirst"': no definition for class "TFFMFirst"
in method for 'convert_motifs' with signature 'motifs="PFMatrix"': no definition for class "PFMatrix"
in method for 'convert_motifs' with signature 'motifs="PWMatrix"': no definition for class "PWMatrix"
in method for 'convert_motifs' with signature 'motifs="ICMatrix"': no definition for class "ICMatrix"
in method for 'convert_motifs' with signature 'motifs="XMatrixList"': no definition for class "XMatrixList"
in method for 'convert_motifs' with signature 'motifs="pwm"': no definition for class "pwm"
in method for 'convert_motifs' with signature 'motifs="pcm"': no definition for class "pcm"
in method for 'convert_motifs' with signature 'motifs="pfm"': no definition for class "pfm"
in method for 'convert_motifs' with signature 'motifs="PWM"': no definition for class "PWM"
in method for 'convert_motifs' with signature 'motifs="Motif"': no definition for class "Motif"
** help
Loading required namespace: universalmotif
*** installing help indices
converting help for package 'universalmotif'
finding HTML links ... done
ArabidopsisMotif html
ArabidopsisPromoters html
finding level-2 HTML links ... done
JASPAR2018_CORE_DBSCORES html
JASPAR2018_CORE_DBSCORES_NORM html
add_multifreq html
compare_motifs html
convert_motifs html
convert_type html
create_motif html
create_sequences html
enrich_motifs html
examplemotif html
examplemotif2 html
filter_motifs html
merge_motifs html
motif_pvalue html
motif_rc html
motif_tree html
read_cisbp html
read_homer html
read_jaspar html
read_matrix html
read_meme html
read_motifs html
read_transfac html
read_uniprobe html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
run_meme html
sample_sites html
scan_sequences html
shuffle_motifs html
shuffle_sequences html
switch_alph html
trim_motifs html
universalmotif-class html
universalmotif-pkg html
utilities html
view_motifs html
write_homer html
write_jaspar html
write_matrix html
write_meme html
write_motifs html
write_transfac html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c add_multifreq_helper.cpp -o add_multifreq_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c motif_simil_helper.cpp -o motif_simil_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c scan_sequences_helper.cpp -o scan_sequences_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c trim_motifs_helper.cpp -o trim_motifs_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c universalmotif_helper.cpp -o universalmotif_helper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o trim_motifs_helper.o universalmotif_helper.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.dll; fi
[[: not found
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.buildbin-libdir/universalmotif/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'universalmotif' as universalmotif_1.0.22.zip
* DONE (universalmotif)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'universalmotif' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
universalmotif.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(universalmotif)
>
> test_check("universalmotif")
== testthat results ===========================================================
OK: 139 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.37 0.28 6.84
|
universalmotif.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(universalmotif)
>
> test_check("universalmotif")
== testthat results ===========================================================
OK: 139 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.87 0.23 5.65
|
|
universalmotif.Rcheck/examples_i386/universalmotif-Ex.timings
|
universalmotif.Rcheck/examples_x64/universalmotif-Ex.timings
|