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This page was generated on 2021-11-26 15:05:45 -0500 (Fri, 26 Nov 2021).

CHECK results for cn.mops on machv2

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- 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? here for more information.
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raw results

Package 348/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.40.0  (landing page)
Gundula Povysil
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_14
git_last_commit: 498dbf7
git_last_commit_date: 2021-10-26 12:01:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.mops
Version: 1.40.0
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_1.40.0.tar.gz
StartedAt: 2021-11-25 15:07:16 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 15:12:19 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 303.3 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_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/cn.mops.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.40.0’
* 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                                    13.236  0.054  29.111
calcFractionalCopyNumbers-CNVDetectionResult-method 11.480  0.093  11.582
calcFractionalCopyNumbers                           11.011  0.035  11.054
cn.mops                                             10.084  0.186  30.013
haplocn.mops                                         1.991  0.034  18.178
getReadCountsFromBAM                                 1.037  0.020   8.843
getSegmentReadCountsFromBAM                          0.587  0.012   8.173
* 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-3.14-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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:208:15: 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/4.1/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
CNVDetectionResult0.0030.0010.003
calcFractionalCopyNumbers-CNVDetectionResult-method11.480 0.09311.582
calcFractionalCopyNumbers11.011 0.03511.054
calcIntegerCopyNumbers-CNVDetectionResult-method0.8760.0080.885
calcIntegerCopyNumbers0.7810.0060.787
cn.mops10.084 0.18630.013
cnvr-CNVDetectionResult-method0.4610.0090.472
cnvr0.4120.0040.417
cnvs-CNVDetectionResult-method0.4470.0030.452
cnvs0.4450.0040.450
exomecn.mops4.7360.0304.770
getReadCountsFromBAM1.0370.0208.843
getSegmentReadCountsFromBAM0.5870.0128.173
gr-CNVDetectionResult-method0.4860.0060.493
gr0.4460.0040.452
haplocn.mops 1.991 0.03418.178
individualCall-CNVDetectionResult-method0.4440.0050.448
individualCall0.4750.0060.480
iniCall-CNVDetectionResult-method0.4380.0060.444
iniCall0.4410.0050.447
integerCopyNumber-CNVDetectionResult-method0.4910.0050.496
integerCopyNumber0.4830.0060.490
localAssessments-CNVDetectionResult-method0.8160.0090.825
localAssessments0.4790.0050.485
makeRobustCNVR0.8350.0070.845
normalizeChromosomes0.3330.0070.341
normalizeGenome0.3310.0090.340
normalizedData-CNVDetectionResult-method0.5130.0120.526
normalizedData0.4570.0050.463
params-CNVDetectionResult-method0.4430.0210.464
params0.4530.0210.474
posteriorProbs-CNVDetectionResult-method0.4380.0040.442
posteriorProbs0.4340.0040.438
referencecn.mops13.236 0.05429.111
sampleNames-CNVDetectionResult-method0.4310.0060.437
sampleNames0.4400.0040.443
segment0.0360.0000.037
segmentation-CNVDetectionResult-method0.4810.0060.488
segmentation0.4590.0070.465
segplot-CNVDetectionResult-method1.7240.0061.730
segplot1.8510.0051.857
singlecn.mops1.5690.0101.580