Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:06:30 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 palomino3


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: 2022-05-17 13:55:01 -0400 (Tue, 17 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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cn.mops_1.42.0.tar.gz
StartedAt: 2022-05-17 22:46:03 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 22:50:12 -0400 (Tue, 17 May 2022)
EllapsedTime: 248.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cn.mops_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/cn.mops/libs/x64/cn.mops.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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                                    15.20   0.00   27.00
calcFractionalCopyNumbers-CNVDetectionResult-method 10.35   0.07   10.43
calcFractionalCopyNumbers                           10.07   0.06   10.13
cn.mops                                              8.58   0.21   24.64
haplocn.mops                                         1.47   0.03   13.36
getReadCountsFromBAM                                 0.53   0.02    5.45
getSegmentReadCountsFromBAM                          0.27   0.00    5.17
* 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
  'F:/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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cn.mops
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cn.mops' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cnmops.cpp -o cnmops.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
   59 |  double globalMean,globalSd,diff,M2,globalVariance;
      |                    ^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
   60 |  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
      |         ^~~~~~~~~~~~
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
   61 |  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
      |                               ^~~~~~~~~~~~
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
   62 |  double newPValue, maxPValue,oldPValue,maxIdx;
      |                                        ^~~~~~
In file included from segment.cpp:10:
F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:210:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
  210 | #define beta  Rf_beta
      |               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
   64 |  double beta,nn;
      |         ^~~~
g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-cn.mops/00new/cn.mops/libs/x64
** 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
** 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
CNVDetectionResult000
calcFractionalCopyNumbers-CNVDetectionResult-method10.35 0.0710.43
calcFractionalCopyNumbers10.07 0.0610.13
calcIntegerCopyNumbers-CNVDetectionResult-method0.530.000.53
calcIntegerCopyNumbers0.470.000.47
cn.mops 8.58 0.2124.64
cnvr-CNVDetectionResult-method0.340.000.34
cnvr0.330.000.33
cnvs-CNVDetectionResult-method0.340.030.37
cnvs0.250.000.25
exomecn.mops3.690.013.71
getReadCountsFromBAM0.530.025.45
getSegmentReadCountsFromBAM0.270.005.17
gr-CNVDetectionResult-method0.210.000.22
gr0.220.000.22
haplocn.mops 1.47 0.0313.36
individualCall-CNVDetectionResult-method0.270.000.26
individualCall0.340.000.35
iniCall-CNVDetectionResult-method0.310.020.33
iniCall0.250.000.25
integerCopyNumber-CNVDetectionResult-method0.300.000.29
integerCopyNumber0.270.010.28
localAssessments-CNVDetectionResult-method0.210.000.22
localAssessments0.330.000.33
makeRobustCNVR0.350.020.36
normalizeChromosomes0.180.000.19
normalizeGenome0.220.010.23
normalizedData-CNVDetectionResult-method0.320.020.33
normalizedData0.280.030.31
params-CNVDetectionResult-method0.220.000.22
params0.180.010.20
posteriorProbs-CNVDetectionResult-method0.320.000.32
posteriorProbs0.250.000.25
referencecn.mops15.2 0.027.0
sampleNames-CNVDetectionResult-method0.190.020.20
sampleNames0.20.00.2
segment0.010.000.02
segmentation-CNVDetectionResult-method0.220.000.22
segmentation0.210.000.20
segplot-CNVDetectionResult-method1.030.021.06
segplot0.920.040.97
singlecn.mops0.750.030.78