Gundula Povysil
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/cn.mops |
| git_branch: RELEASE_3_17 |
| git_last_commit: baa7ea0 |
| git_last_commit_date: 2023-04-25 10:21:44 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -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 375/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.mops 1.46.0 (landing page) Gundula Povysil
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the cn.mops 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: cn.mops |
| Version: 1.46.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.46.0.tar.gz |
| StartedAt: 2023-10-17 10:30:09 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 10:36:03 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 354.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cn.mops.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 ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.46.0’
* 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 ‘cn.mops’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
referencecn.mops 8.449 0.084 32.237
cn.mops 6.663 0.152 34.393
calcFractionalCopyNumbers-CNVDetectionResult-method 6.551 0.088 10.292
calcFractionalCopyNumbers 6.293 0.060 9.856
haplocn.mops 1.289 0.042 21.780
getReadCountsFromBAM 0.524 0.023 10.308
getSegmentReadCountsFromBAM 0.326 0.016 9.846
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cn.mops.Rcheck/00check.log’
for details.
cn.mops.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.mops
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cnmops.cpp -o cnmops.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.cpp -o segment.o
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
^
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
double beta,nn;
^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta'
#define beta Rf_beta
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -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 cn.mops.so R_init_cnmops.o cnmops.o segment.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-cn.mops/00new/cn.mops/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 (cn.mops)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0.002 | 0.001 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 6.551 | 0.088 | 10.292 | |
| calcFractionalCopyNumbers | 6.293 | 0.060 | 9.856 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.503 | 0.010 | 0.809 | |
| calcIntegerCopyNumbers | 0.483 | 0.011 | 0.759 | |
| cn.mops | 6.663 | 0.152 | 34.393 | |
| cnvr-CNVDetectionResult-method | 0.270 | 0.008 | 0.423 | |
| cnvr | 0.247 | 0.006 | 0.389 | |
| cnvs-CNVDetectionResult-method | 0.259 | 0.007 | 0.410 | |
| cnvs | 0.268 | 0.008 | 0.429 | |
| exomecn.mops | 2.871 | 0.044 | 4.502 | |
| getReadCountsFromBAM | 0.524 | 0.023 | 10.308 | |
| getSegmentReadCountsFromBAM | 0.326 | 0.016 | 9.846 | |
| gr-CNVDetectionResult-method | 0.272 | 0.008 | 0.447 | |
| gr | 0.277 | 0.007 | 0.446 | |
| haplocn.mops | 1.289 | 0.042 | 21.780 | |
| individualCall-CNVDetectionResult-method | 0.287 | 0.008 | 0.455 | |
| individualCall | 0.271 | 0.007 | 0.427 | |
| iniCall-CNVDetectionResult-method | 0.271 | 0.007 | 0.440 | |
| iniCall | 0.274 | 0.007 | 0.459 | |
| integerCopyNumber-CNVDetectionResult-method | 0.277 | 0.008 | 0.448 | |
| integerCopyNumber | 0.275 | 0.008 | 0.434 | |
| localAssessments-CNVDetectionResult-method | 0.592 | 0.015 | 0.937 | |
| localAssessments | 0.257 | 0.008 | 0.410 | |
| makeRobustCNVR | 0.462 | 0.010 | 0.727 | |
| normalizeChromosomes | 0.179 | 0.010 | 0.289 | |
| normalizeGenome | 0.164 | 0.009 | 0.264 | |
| normalizedData-CNVDetectionResult-method | 0.277 | 0.011 | 0.443 | |
| normalizedData | 0.284 | 0.008 | 0.443 | |
| params-CNVDetectionResult-method | 0.243 | 0.016 | 0.403 | |
| params | 0.247 | 0.016 | 0.401 | |
| posteriorProbs-CNVDetectionResult-method | 0.242 | 0.007 | 0.381 | |
| posteriorProbs | 0.265 | 0.008 | 0.417 | |
| referencecn.mops | 8.449 | 0.084 | 32.237 | |
| sampleNames-CNVDetectionResult-method | 0.254 | 0.009 | 0.404 | |
| sampleNames | 0.257 | 0.007 | 0.404 | |
| segment | 0.026 | 0.001 | 0.046 | |
| segmentation-CNVDetectionResult-method | 0.245 | 0.008 | 0.383 | |
| segmentation | 0.263 | 0.008 | 0.438 | |
| segplot-CNVDetectionResult-method | 1.109 | 0.015 | 1.781 | |
| segplot | 1.136 | 0.016 | 1.774 | |
| singlecn.mops | 0.778 | 0.013 | 1.209 | |