| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:56 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the universalmotif package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/universalmotif.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 2038/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.13.9 (landing page) Benjamin Jean-Marie Tremblay
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: universalmotif |
| Version: 1.13.9 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:universalmotif.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings universalmotif_1.13.9.tar.gz |
| StartedAt: 2022-03-17 20:34:07 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:36:52 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: universalmotif.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:universalmotif.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings universalmotif_1.13.9.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/universalmotif.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.13.9'
* package encoding: UTF-8
* 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 'universalmotif' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.7Mb
libs 1.7Mb
* 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/universalmotif/libs/x64/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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
convert_motifs 6.22 0.42 6.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/universalmotif.Rcheck/00check.log'
for details.
universalmotif.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL universalmotif
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'universalmotif' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c add_multifreq.cpp -o add_multifreq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c calc_complexity.cpp -o calc_complexity.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c compare_motifs.cpp -o compare_motifs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c get_bkg.cpp -o get_bkg.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c motif_finder.cpp -o motif_finder.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c motif_peaks.cpp -o motif_peaks.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c motif_pvalue.cpp -o motif_pvalue.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c scan_sequences.cpp -o scan_sequences.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c shuffle_sequences.cpp -o shuffle_sequences.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c trim_motifs.cpp -o trim_motifs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c universalmotif-class.cpp -o universalmotif-class.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils-exported.cpp -o utils-exported.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils-internal.cpp -o utils-internal.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq.o calc_complexity.o compare_motifs.o get_bkg.o motif_finder.o motif_peaks.o motif_pvalue.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-universalmotif/00new/universalmotif/libs/x64
** 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
*** 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
add_multifreq html
compare_motifs html
convert_motifs html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-universalmotif/00new/universalmotif/help/convert_motifs+2CPWM-method.html
convert_type html
create_motif html
create_sequences html
enrich_motifs html
examplemotif html
examplemotif2 html
filter_motifs html
fontDFroboto html
get_bkg html
make_DBscores html
merge_motifs html
merge_similar html
motif_peaks 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
run_meme html
sample_sites html
scan_sequences html
sequence_complexity html
shuffle_motifs html
shuffle_sequences html
switch_alph html
tidy-motifs html
trim_motifs html
universalmotif-class html
universalmotif-pkg html
utilities html
utils-motif html
utils-sequence html
view_logo 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (universalmotif)
Making 'packages.html' ... done
universalmotif.Rcheck/tests/spelling.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.14 0.06 0.18
universalmotif.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.
> if (R.Version()$arch != "i386") {
+
+ library(testthat)
+ library(universalmotif)
+
+ test_check("universalmotif")
+
+ } else TRUE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ]
>
> proc.time()
user system elapsed
8.26 0.53 8.78
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.01 | 0.00 | 0.02 | |
| compare_motifs | 0.11 | 0.00 | 0.10 | |
| convert_motifs | 6.22 | 0.42 | 6.65 | |
| convert_type | 0 | 0 | 0 | |
| create_motif | 0.21 | 0.02 | 0.24 | |
| create_sequences | 0 | 0 | 0 | |
| enrich_motifs | 1.43 | 0.12 | 1.54 | |
| filter_motifs | 0.01 | 0.00 | 0.02 | |
| get_bkg | 0.17 | 0.02 | 0.19 | |
| make_DBscores | 0 | 0 | 0 | |
| merge_motifs | 0.11 | 0.00 | 0.11 | |
| merge_similar | 0 | 0 | 0 | |
| motif_peaks | 0.14 | 0.03 | 0.17 | |
| motif_pvalue | 0.08 | 0.00 | 0.08 | |
| motif_rc | 0 | 0 | 0 | |
| motif_tree | 0.23 | 0.05 | 0.28 | |
| read_cisbp | 0 | 0 | 0 | |
| read_homer | 0.17 | 0.01 | 0.19 | |
| read_jaspar | 0 | 0 | 0 | |
| read_matrix | 0.02 | 0.00 | 0.01 | |
| read_meme | 0 | 0 | 0 | |
| read_transfac | 0.02 | 0.00 | 0.02 | |
| read_uniprobe | 0 | 0 | 0 | |
| run_meme | 0 | 0 | 0 | |
| sample_sites | 0.01 | 0.00 | 0.02 | |
| scan_sequences | 0.56 | 0.03 | 0.59 | |
| sequence_complexity | 0.71 | 0.03 | 0.73 | |
| shuffle_sequences | 0 | 0 | 0 | |
| switch_alph | 0 | 0 | 0 | |
| tidy-motifs | 0 | 0 | 0 | |
| trim_motifs | 0 | 0 | 0 | |
| universalmotif-class | 0.01 | 0.00 | 0.02 | |
| utils-motif | 0.10 | 0.06 | 0.15 | |
| utils-sequence | 0.45 | 0.02 | 0.47 | |
| view_logo | 0.09 | 0.00 | 0.09 | |
| view_motifs | 0.08 | 0.01 | 0.10 | |
| write_homer | 0 | 0 | 0 | |
| write_jaspar | 0 | 0 | 0 | |
| write_matrix | 0 | 0 | 0 | |
| write_meme | 0 | 0 | 0 | |
| write_transfac | 0.01 | 0.00 | 0.02 | |