Vivek Kohar
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/sRACIPE |
| git_branch: RELEASE_3_17 |
| git_last_commit: a4ae73b |
| git_last_commit_date: 2023-04-25 11:09:28 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2006/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sRACIPE 1.16.0 (landing page) Vivek Kohar
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the sRACIPE 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: sRACIPE |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sRACIPE_1.16.0.tar.gz |
| StartedAt: 2023-10-19 04:29:40 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 04:35:17 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 337.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sRACIPE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sRACIPE_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sRACIPE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRACIPE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRACIPE’ version ‘1.16.0’
* 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 ‘sRACIPE’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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 ... NOTE
sracipeSimulate: no visible global function definition for
‘registerDoFuture’
sracipeSimulate: no visible global function definition for ‘plan’
sracipeSimulate: no visible global function definition for ‘%dopar%’
sracipeSimulate: no visible global function definition for ‘foreach’
sracipeSimulate: no visible binding for global variable
‘configurationTmp’
sracipeSimulate: no visible binding for global variable ‘outFileGETmp’
sracipeSimulate: no visible binding for global variable
‘outFileParamsTmp’
sracipeSimulate: no visible binding for global variable ‘outFileICTmp’
Undefined global functions or variables:
%dopar% configurationTmp foreach outFileGETmp outFileICTmp
outFileParamsTmp plan registerDoFuture
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sracipeSimulate 15.905 0.116 28.695
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sRACIPE.Rcheck/00check.log’
for details.
sRACIPE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sRACIPE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘sRACIPE’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ 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/4.3-arm64/Resources/library/Rcpp/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/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateThresholds.cpp -o generateThresholds.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c header.cpp -o header.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simulateGRC.cpp -o simulateGRC.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c steppers.cpp -o steppers.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-sRACIPE/00new/sRACIPE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (sRACIPE)
sRACIPE.Rcheck/sRACIPE-Ex.timings
| name | user | system | elapsed | |
| RacipeSE | 0.045 | 0.002 | 0.087 | |
| annotation-RacipeSE-method | 0.908 | 0.025 | 1.679 | |
| annotation-set-RacipeSE-ANY-method | 0.853 | 0.014 | 1.539 | |
| sracipeCircuit-set | 0.038 | 0.004 | 0.076 | |
| sracipeCircuit | 0.037 | 0.003 | 0.073 | |
| sracipeConfig-set | 0.009 | 0.002 | 0.017 | |
| sracipeConfig | 0.034 | 0.005 | 0.067 | |
| sracipeGenParamNames | 0.037 | 0.004 | 0.069 | |
| sracipeGetTS | 0.096 | 0.010 | 0.195 | |
| sracipeIC-set | 0.144 | 0.008 | 0.271 | |
| sracipeIC | 0.086 | 0.007 | 0.167 | |
| sracipeKnockDown | 0.001 | 0.002 | 0.002 | |
| sracipeNormalize | 0.121 | 0.008 | 0.239 | |
| sracipeOverExp | 0.001 | 0.002 | 0.007 | |
| sracipeParams-set | 0.099 | 0.006 | 0.178 | |
| sracipeParams | 0.087 | 0.007 | 0.174 | |
| sracipePlotCircuit | 0.002 | 0.002 | 0.005 | |
| sracipePlotData | 0.002 | 0.002 | 0.007 | |
| sracipePlotParamBifur | 0.002 | 0.002 | 0.008 | |
| sracipeSimulate | 15.905 | 0.116 | 28.695 | |