Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:07:48 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for cn.mops on merida1


To the developers/maintainers of the cn.mops package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cn.mops.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 356/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.42.0  (landing page)
Gundula Povysil
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_15
git_last_commit: 64e5afb
git_last_commit_date: 2022-04-26 11:09:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.mops
Version: 1.42.0
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_1.42.0.tar.gz
StartedAt: 2022-05-20 00:27:31 -0400 (Fri, 20 May 2022)
EndedAt: 2022-05-20 00:33:47 -0400 (Fri, 20 May 2022)
EllapsedTime: 376.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.42.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* 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 ‘1.42.0’
* 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
* 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 ... 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                                    14.277  0.065  34.271
calcFractionalCopyNumbers-CNVDetectionResult-method 12.241  0.080  12.821
cn.mops                                             11.924  0.227  37.302
calcFractionalCopyNumbers                           11.414  0.141  12.035
exomecn.mops                                         5.384  0.031   5.728
haplocn.mops                                         2.182  0.029  22.594
getReadCountsFromBAM                                 0.946  0.017  10.688
getSegmentReadCountsFromBAM                          0.566  0.012  10.199
* 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-3.15-bioc/meat/cn.mops.Rcheck/00check.log’
for details.



Installation output

cn.mops.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.mops
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cnmops.cpp -o cnmops.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c segment.cpp -o segment.o
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
                        ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/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)

Tests output


Example timings

cn.mops.Rcheck/cn.mops-Ex.timings

nameusersystemelapsed
CNVDetectionResult0.0020.0010.003
calcFractionalCopyNumbers-CNVDetectionResult-method12.241 0.08012.821
calcFractionalCopyNumbers11.414 0.14112.035
calcIntegerCopyNumbers-CNVDetectionResult-method0.8600.0070.915
calcIntegerCopyNumbers0.7640.0100.776
cn.mops11.924 0.22737.302
cnvr-CNVDetectionResult-method0.8430.0150.875
cnvr0.4430.0050.480
cnvs-CNVDetectionResult-method0.4420.0050.456
cnvs0.4690.0110.503
exomecn.mops5.3840.0315.728
getReadCountsFromBAM 0.946 0.01710.688
getSegmentReadCountsFromBAM 0.566 0.01210.199
gr-CNVDetectionResult-method0.4400.0050.453
gr0.4530.0040.479
haplocn.mops 2.182 0.02922.594
individualCall-CNVDetectionResult-method0.4640.0060.480
individualCall0.4530.0040.483
iniCall-CNVDetectionResult-method0.4640.0040.487
iniCall0.4730.0050.507
integerCopyNumber-CNVDetectionResult-method0.4580.0060.494
integerCopyNumber0.4590.0050.494
localAssessments-CNVDetectionResult-method0.4600.0040.469
localAssessments0.4600.0050.469
makeRobustCNVR0.8300.0060.884
normalizeChromosomes0.7860.0120.856
normalizeGenome0.3580.0090.382
normalizedData-CNVDetectionResult-method0.4470.0040.455
normalizedData0.4420.0050.452
params-CNVDetectionResult-method0.4520.0200.494
params0.4290.0130.487
posteriorProbs-CNVDetectionResult-method0.4290.0040.467
posteriorProbs0.4420.0040.475
referencecn.mops14.277 0.06534.271
sampleNames-CNVDetectionResult-method0.4280.0040.435
sampleNames0.4240.0040.450
segment0.0400.0010.042
segmentation-CNVDetectionResult-method0.4430.0050.477
segmentation0.4390.0040.459
segplot-CNVDetectionResult-method1.8800.0081.987
segplot1.9110.0092.016
singlecn.mops1.6170.0071.707