Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-04 11:06:01 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 355/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.45.0  (landing page)
Gundula Povysil
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: master
git_last_commit: 0617906
git_last_commit_date: 2022-11-01 11:06:31 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.45.0
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_1.45.0.tar.gz
StartedAt: 2023-02-03 23:43:48 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 23:52:23 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 515.0 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_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* 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 ‘1.45.0’
* 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 11.0.0 (clang-1100.0.33.17)’
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used 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 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                                    14.369  0.068  43.984
calcFractionalCopyNumbers-CNVDetectionResult-method 11.917  0.082  17.643
cn.mops                                             11.651  0.194  51.035
calcFractionalCopyNumbers                           11.584  0.043  17.112
exomecn.mops                                         5.279  0.025   7.852
haplocn.mops                                         2.165  0.030  30.153
getReadCountsFromBAM                                 0.894  0.017  15.038
getSegmentReadCountsFromBAM                          0.554  0.010  14.065
* 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/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/4.3/Resources/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
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/4.3/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
CNVDetectionResult0.0020.0010.006
calcFractionalCopyNumbers-CNVDetectionResult-method11.917 0.08217.643
calcFractionalCopyNumbers11.584 0.04317.112
calcIntegerCopyNumbers-CNVDetectionResult-method0.9430.0091.428
calcIntegerCopyNumbers0.8100.0121.175
cn.mops11.651 0.19451.035
cnvr-CNVDetectionResult-method0.4330.0070.624
cnvr0.8150.0121.223
cnvs-CNVDetectionResult-method0.4440.0040.656
cnvs0.4330.0040.665
exomecn.mops5.2790.0257.852
getReadCountsFromBAM 0.894 0.01715.038
getSegmentReadCountsFromBAM 0.554 0.01014.065
gr-CNVDetectionResult-method0.4500.0070.783
gr0.4570.0040.633
haplocn.mops 2.165 0.03030.153
individualCall-CNVDetectionResult-method0.4510.0050.626
individualCall0.4820.0060.754
iniCall-CNVDetectionResult-method0.4600.0050.620
iniCall0.4530.0040.609
integerCopyNumber-CNVDetectionResult-method0.4770.0040.677
integerCopyNumber0.4460.0050.609
localAssessments-CNVDetectionResult-method0.4640.0060.650
localAssessments0.4710.0060.650
makeRobustCNVR0.8260.0071.193
normalizeChromosomes0.3690.0100.486
normalizeGenome0.7470.0141.014
normalizedData-CNVDetectionResult-method0.4560.0080.629
normalizedData0.4620.0060.652
params-CNVDetectionResult-method0.4300.0140.612
params0.4460.0150.624
posteriorProbs-CNVDetectionResult-method0.4240.0060.625
posteriorProbs0.4300.0050.577
referencecn.mops14.369 0.06843.984
sampleNames-CNVDetectionResult-method0.4200.0040.476
sampleNames0.4320.0050.567
segment0.040.000.06
segmentation-CNVDetectionResult-method0.4450.0040.595
segmentation0.4290.0040.575
segplot-CNVDetectionResult-method1.9280.0092.489
segplot1.8990.0082.512
singlecn.mops1.6320.0082.225