Gundula Povysil
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/cn.mops |
| git_branch: devel |
| git_last_commit: ee78d2e |
| git_last_commit_date: 2024-04-30 10:26:19 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:09 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 376/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.mops 1.51.0 (landing page) Gundula Povysil
| kjohnson1 | macOS 13.6.6 Ventura / 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: 1.51.0 |
| 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_1.51.0.tar.gz |
| StartedAt: 2024-05-19 08:51:32 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 08:55:10 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 219.0 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_1.51.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/cn.mops.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* 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 ‘1.51.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 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 whether 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 8.164 0.070 18.704
calcFractionalCopyNumbers-CNVDetectionResult-method 6.224 0.052 6.736
cn.mops 5.608 0.139 18.555
calcFractionalCopyNumbers 4.997 0.036 5.107
haplocn.mops 1.067 0.045 12.234
getReadCountsFromBAM 0.458 0.028 6.185
getSegmentReadCountsFromBAM 0.307 0.021 6.102
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
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:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^
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:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^
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 -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/4.4-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 | 0.003 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 6.224 | 0.052 | 6.736 | |
| calcFractionalCopyNumbers | 4.997 | 0.036 | 5.107 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.428 | 0.005 | 0.437 | |
| calcIntegerCopyNumbers | 0.380 | 0.006 | 0.388 | |
| cn.mops | 5.608 | 0.139 | 18.555 | |
| cnvr-CNVDetectionResult-method | 0.229 | 0.006 | 0.241 | |
| cnvr | 0.720 | 0.011 | 0.740 | |
| cnvs-CNVDetectionResult-method | 0.236 | 0.005 | 0.241 | |
| cnvs | 0.222 | 0.004 | 0.227 | |
| exomecn.mops | 2.304 | 0.023 | 2.344 | |
| getReadCountsFromBAM | 0.458 | 0.028 | 6.185 | |
| getSegmentReadCountsFromBAM | 0.307 | 0.021 | 6.102 | |
| gr-CNVDetectionResult-method | 0.240 | 0.006 | 0.255 | |
| gr | 0.240 | 0.005 | 0.245 | |
| haplocn.mops | 1.067 | 0.045 | 12.234 | |
| individualCall-CNVDetectionResult-method | 0.232 | 0.005 | 0.239 | |
| individualCall | 0.240 | 0.005 | 0.246 | |
| iniCall-CNVDetectionResult-method | 0.233 | 0.005 | 0.239 | |
| iniCall | 0.231 | 0.005 | 0.236 | |
| integerCopyNumber-CNVDetectionResult-method | 0.251 | 0.005 | 0.257 | |
| integerCopyNumber | 0.229 | 0.004 | 0.235 | |
| localAssessments-CNVDetectionResult-method | 0.277 | 0.016 | 0.296 | |
| localAssessments | 0.273 | 0.009 | 0.283 | |
| makeRobustCNVR | 0.396 | 0.005 | 0.405 | |
| normalizeChromosomes | 0.169 | 0.013 | 0.184 | |
| normalizeGenome | 0.176 | 0.012 | 0.189 | |
| normalizedData-CNVDetectionResult-method | 0.241 | 0.005 | 0.246 | |
| normalizedData | 0.248 | 0.007 | 0.254 | |
| params-CNVDetectionResult-method | 0.236 | 0.015 | 0.251 | |
| params | 0.228 | 0.015 | 0.244 | |
| posteriorProbs-CNVDetectionResult-method | 0.239 | 0.005 | 0.247 | |
| posteriorProbs | 0.222 | 0.004 | 0.228 | |
| referencecn.mops | 8.164 | 0.070 | 18.704 | |
| sampleNames-CNVDetectionResult-method | 0.216 | 0.005 | 0.252 | |
| sampleNames | 0.232 | 0.005 | 0.240 | |
| segment | 0.019 | 0.000 | 0.022 | |
| segmentation-CNVDetectionResult-method | 0.228 | 0.005 | 0.240 | |
| segmentation | 0.249 | 0.005 | 0.277 | |
| segplot-CNVDetectionResult-method | 1.394 | 0.012 | 1.443 | |
| segplot | 0.920 | 0.008 | 0.934 | |
| singlecn.mops | 0.705 | 0.007 | 0.714 | |