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This page was generated on 2022-01-21 11:11:03 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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? here 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 345/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.41.1  (landing page)
Gundula Povysil
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: master
git_last_commit: cd0cc29
git_last_commit_date: 2021-11-20 03:52:29 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.mops
Version: 1.41.1
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_1.41.1.tar.gz
StartedAt: 2022-01-20 23:24:32 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 23:30:53 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 381.2 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_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.41.1’
* 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                                    14.439  0.057  33.625
calcFractionalCopyNumbers-CNVDetectionResult-method 12.227  0.103  12.917
calcFractionalCopyNumbers                           11.328  0.054  11.848
cn.mops                                             10.559  0.177  33.993
exomecn.mops                                         4.970  0.026   5.258
haplocn.mops                                         2.109  0.029  20.923
getReadCountsFromBAM                                 0.878  0.019   9.830
getSegmentReadCountsFromBAM                          0.537  0.013   9.492
* 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-3.15-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
###
##############################################################################
##############################################################################


* 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:209:15: 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
CNVDetectionResult0.0020.0000.003
calcFractionalCopyNumbers-CNVDetectionResult-method12.227 0.10312.917
calcFractionalCopyNumbers11.328 0.05411.848
calcIntegerCopyNumbers-CNVDetectionResult-method0.8380.0060.886
calcIntegerCopyNumbers1.1600.0061.208
cn.mops10.559 0.17733.993
cnvr-CNVDetectionResult-method0.4180.0060.435
cnvr0.4360.0070.464
cnvs-CNVDetectionResult-method0.4210.0050.442
cnvs0.8380.0130.893
exomecn.mops4.9700.0265.258
getReadCountsFromBAM0.8780.0199.830
getSegmentReadCountsFromBAM0.5370.0139.492
gr-CNVDetectionResult-method0.4330.0040.440
gr0.4350.0040.470
haplocn.mops 2.109 0.02920.923
individualCall-CNVDetectionResult-method0.4530.0050.470
individualCall0.4410.0050.471
iniCall-CNVDetectionResult-method0.4480.0050.469
iniCall0.4490.0040.476
integerCopyNumber-CNVDetectionResult-method0.4340.0050.470
integerCopyNumber0.4460.0060.467
localAssessments-CNVDetectionResult-method0.4340.0050.457
localAssessments0.4440.0050.476
makeRobustCNVR0.7740.0050.813
normalizeChromosomes0.3900.0100.423
normalizeGenome0.3760.0110.408
normalizedData-CNVDetectionResult-method0.4360.0050.465
normalizedData0.4540.0110.487
params-CNVDetectionResult-method0.4100.0130.447
params0.4260.0140.461
posteriorProbs-CNVDetectionResult-method0.4060.0040.422
posteriorProbs0.4210.0040.446
referencecn.mops14.439 0.05733.625
sampleNames-CNVDetectionResult-method0.4170.0060.431
sampleNames0.4050.0040.426
segment0.0400.0010.040
segmentation-CNVDetectionResult-method0.4270.0050.436
segmentation0.3990.0040.403
segplot-CNVDetectionResult-method1.7510.0061.760
segplot1.7760.0071.785
singlecn.mops1.5080.0061.516