| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:49 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 | ||||
| Package 2241/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.22.0 (landing page) Benjamin Jean-Marie Tremblay
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the universalmotif package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: universalmotif |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings universalmotif_1.22.0.tar.gz |
| StartedAt: 2024-05-07 01:41:20 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:42:17 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 56.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: universalmotif.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings universalmotif_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/universalmotif.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘universalmotif’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 code 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ... 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
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/universalmotif.Rcheck/00check.log’
for details.
universalmotif.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL universalmotif
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c add_multifreq.cpp -o add_multifreq.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calc_complexity.cpp -o calc_complexity.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compare_motifs.cpp -o compare_motifs.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c get_bkg.cpp -o get_bkg.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c motif_finder.cpp -o motif_finder.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c motif_peaks.cpp -o motif_peaks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c motif_pvalue.cpp -o motif_pvalue.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scan_sequences.cpp -o scan_sequences.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c shuffle_sequences.cpp -o shuffle_sequences.o
shuffle_sequences.cpp:104:20: warning: variable 'vertex_ok' set but not used [-Wunused-but-set-variable]
int counter = 0, vertex_ok = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trim_motifs.cpp -o trim_motifs.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c universalmotif-class.cpp -o universalmotif-class.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils-exported.cpp -o utils-exported.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils-internal.cpp -o utils-internal.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o universalmotif.so 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 -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-universalmotif/00new/universalmotif/libs
** 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
** 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 (universalmotif)
universalmotif.Rcheck/tests/spelling.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
0.071 0.020 0.089
universalmotif.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 2 | SKIP 0 | PASS 240 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 240 ]
>
> proc.time()
user system elapsed
2.714 0.190 2.904
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.004 | 0.001 | 0.005 | |
| compare_motifs | 0.044 | 0.001 | 0.045 | |
| convert_motifs | 4.262 | 0.097 | 4.362 | |
| convert_type | 0.003 | 0.000 | 0.003 | |
| create_motif | 0.082 | 0.004 | 0.087 | |
| create_sequences | 0.001 | 0.000 | 0.002 | |
| enrich_motifs | 0.326 | 0.018 | 0.346 | |
| filter_motifs | 0.005 | 0.000 | 0.006 | |
| get_bkg | 0.066 | 0.004 | 0.070 | |
| make_DBscores | 0 | 0 | 0 | |
| merge_motifs | 0.065 | 0.005 | 0.071 | |
| merge_similar | 0 | 0 | 0 | |
| motif_peaks | 0.064 | 0.006 | 0.071 | |
| motif_pvalue | 0.032 | 0.007 | 0.039 | |
| motif_rc | 0.001 | 0.000 | 0.002 | |
| motif_tree | 0.106 | 0.010 | 0.116 | |
| read_cisbp | 0.001 | 0.000 | 0.001 | |
| read_homer | 0.064 | 0.003 | 0.066 | |
| read_jaspar | 0.001 | 0.000 | 0.001 | |
| read_matrix | 0.001 | 0.000 | 0.001 | |
| read_meme | 0.006 | 0.001 | 0.006 | |
| read_transfac | 0.003 | 0.000 | 0.003 | |
| read_uniprobe | 0.003 | 0.001 | 0.003 | |
| run_meme | 0 | 0 | 0 | |
| sample_sites | 0.005 | 0.000 | 0.005 | |
| scan_sequences | 0.227 | 0.008 | 0.234 | |
| sequence_complexity | 0.284 | 0.010 | 0.294 | |
| shuffle_sequences | 0.002 | 0.000 | 0.002 | |
| switch_alph | 0.000 | 0.000 | 0.001 | |
| tidy-motifs | 0 | 0 | 0 | |
| trim_motifs | 0.002 | 0.000 | 0.002 | |
| universalmotif-class | 0.004 | 0.001 | 0.005 | |
| utils-motif | 0.024 | 0.051 | 0.076 | |
| utils-sequence | 0.162 | 0.005 | 0.166 | |
| view_logo | 0.078 | 0.005 | 0.083 | |
| view_motifs | 0.034 | 0.002 | 0.036 | |
| write_homer | 0.001 | 0.000 | 0.001 | |
| write_jaspar | 0.003 | 0.000 | 0.003 | |
| write_matrix | 0.000 | 0.001 | 0.001 | |
| write_meme | 0.004 | 0.000 | 0.004 | |
| write_transfac | 0.002 | 0.000 | 0.002 | |