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This page was generated on 2021-09-24 15:06:36 -0400 (Fri, 24 Sep 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 340/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.38.0  (landing page)
Gundula Povysil
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_13
git_last_commit: c1ccf44
git_last_commit_date: 2021-05-19 11:50:48 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.mops_1.38.0.tar.gz
StartedAt: 2021-09-23 17:27:30 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 17:32:17 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 286.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.mops_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.38.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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                                    12.548  0.041  27.594
cn.mops                                             10.314  0.170  28.580
calcFractionalCopyNumbers                           10.091  0.024  10.119
calcFractionalCopyNumbers-CNVDetectionResult-method  9.990  0.054  10.050
haplocn.mops                                         2.265  0.045  17.554
getReadCountsFromBAM                                 0.948  0.016   8.329
getSegmentReadCountsFromBAM                          0.563  0.012   8.007
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/Versions/Current/Resources/bin/R CMD INSTALL cn.mops
###
##############################################################################
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* 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:212:15: 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
CNVDetectionResult0.0010.0010.003
calcFractionalCopyNumbers-CNVDetectionResult-method 9.990 0.05410.050
calcFractionalCopyNumbers10.091 0.02410.119
calcIntegerCopyNumbers-CNVDetectionResult-method1.0270.0081.036
calcIntegerCopyNumbers0.8980.0100.909
cn.mops10.314 0.17028.580
cnvr-CNVDetectionResult-method0.3110.0040.314
cnvr0.3900.0050.396
cnvs-CNVDetectionResult-method0.4340.0050.439
cnvs0.4250.0040.429
exomecn.mops4.3390.0394.388
getReadCountsFromBAM0.9480.0168.329
getSegmentReadCountsFromBAM0.5630.0128.007
gr-CNVDetectionResult-method0.4090.0040.414
gr0.4100.0030.413
haplocn.mops 2.265 0.04517.554
individualCall-CNVDetectionResult-method0.3950.0050.401
individualCall0.4090.0050.414
iniCall-CNVDetectionResult-method0.3940.0030.398
iniCall0.3550.0020.358
integerCopyNumber-CNVDetectionResult-method0.4300.0050.435
integerCopyNumber0.4910.0050.496
localAssessments-CNVDetectionResult-method0.4480.0050.454
localAssessments0.4650.0050.470
makeRobustCNVR0.9190.0050.925
normalizeChromosomes0.2900.0090.298
normalizeGenome0.3350.0120.347
normalizedData-CNVDetectionResult-method0.4510.0150.466
normalizedData0.4700.0050.476
params-CNVDetectionResult-method0.3950.0190.415
params0.4240.0150.440
posteriorProbs-CNVDetectionResult-method0.4300.0030.434
posteriorProbs0.3610.0030.366
referencecn.mops12.548 0.04127.594
sampleNames-CNVDetectionResult-method0.4190.0060.426
sampleNames0.4360.0040.440
segment0.0420.0010.043
segmentation-CNVDetectionResult-method0.4290.0060.436
segmentation0.4500.0060.455
segplot-CNVDetectionResult-method1.8340.0061.839
segplot1.3950.0051.401
singlecn.mops1.3930.0051.398