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This page was generated on 2021-09-20 15:05:09 -0400 (Mon, 20 Sep 2021).

CHECK results for cn.mops on tokay2

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.
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raw results

Package 340/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.38.0  (landing page)
Gundula Povysil
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cn.mops.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cn.mops_1.38.0.tar.gz
StartedAt: 2021-09-19 20:35:37 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 20:42:26 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 408.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cn.mops.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cn.mops_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cn.mops/libs/i386/cn.mops.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-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)
  Found 'printf', possibly from 'printf' (C)

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    18.42   0.02   30.64
calcFractionalCopyNumbers-CNVDetectionResult-method 12.49   0.03   12.51
calcFractionalCopyNumbers                           12.18   0.00   12.17
cn.mops                                              8.81   0.33   22.83
haplocn.mops                                         1.50   0.03   12.45
getReadCountsFromBAM                                 0.86   0.01    7.61
getSegmentReadCountsFromBAM                          0.48   0.02    5.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    17.47   0.00   28.61
calcFractionalCopyNumbers                           12.33   0.08   12.41
calcFractionalCopyNumbers-CNVDetectionResult-method 11.28   0.02   11.29
cn.mops                                              9.08   0.11   23.36
haplocn.mops                                         1.46   0.01   11.75
getReadCountsFromBAM                                 0.98   0.00    7.58
getSegmentReadCountsFromBAM                          0.53   0.00    5.94
* 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
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cn.mops_1.38.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.38.0.zip && rm cn.mops_1.38.0.tar.gz cn.mops_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 16  630k   16  101k    0     0   536k      0  0:00:01 --:--:--  0:00:01  537k
100  630k  100  630k    0     0  1089k      0 --:--:-- --:--:-- --:--:-- 1089k

install for i386

* installing *source* package 'cn.mops' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/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]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^~~~~~~~~~~~
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^~~~~~~~~~~~
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^~~~~~
In file included from segment.cpp:10:
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
 #define beta  Rf_beta
               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
  double beta,nn;
         ^~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.mops'
    finding HTML links ... done
    CNVDetectionResult                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/cnvdetectionresult.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/help/CnvDetectionResult.html
    CNVRanges                               html  
    X                                       html  
    XRanges                                 html  
    calcFractionalCopyNumbers-CNVDetectionResult-method
                                            html  
    calcFractionalCopyNumbers               html  
    calcIntegerCopyNumbers-CNVDetectionResult-method
                                            html  
    calcIntegerCopyNumbers                  html  
    cn.mops                                 html  
    cnvr-CNVDetectionResult-method          html  
    cnvr                                    html  
    cnvs-CNVDetectionResult-method          html  
    cnvs                                    html  
    exomeCounts                             html  
    exomecn.mops                            html  
    getReadCountsFromBAM                    html  
    getSegmentReadCountsFromBAM             html  
    gr-CNVDetectionResult-method            html  
    gr                                      html  
    haplocn.mops                            html  
    individualCall-CNVDetectionResult-method
                                            html  
    individualCall                          html  
    iniCall-CNVDetectionResult-method       html  
    iniCall                                 html  
    integerCopyNumber-CNVDetectionResult-method
                                            html  
    integerCopyNumber                       html  
    localAssessments-CNVDetectionResult-method
                                            html  
    localAssessments                        html  
    makeRobustCNVR                          html  
    normalizeChromosomes                    html  
    normalizeGenome                         html  
    normalizedData-CNVDetectionResult-method
                                            html  
    normalizedData                          html  
    params-CNVDetectionResult-method        html  
    params                                  html  
    plot                                    html  
    posteriorProbs-CNVDetectionResult-method
                                            html  
    posteriorProbs                          html  
    referencecn.mops                        html  
    sampleNames-CNVDetectionResult-method   html  
    sampleNames                             html  
    segment                                 html  
    segmentation-CNVDetectionResult-method
                                            html  
    segmentation                            html  
    segplot-CNVDetectionResult-method       html  
    segplot                                 html  
    show                                    html  
    singlecn.mops                           html  
** 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

install for x64

* installing *source* package 'cn.mops' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/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]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^~~~~~~~~~~~
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^~~~~~~~~~~~
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^~~~~~
In file included from segment.cpp:10:
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
 #define beta  Rf_beta
               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
  double beta,nn;
         ^~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.38.0.zip
* DONE (cn.mops)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'cn.mops' successfully unpacked and MD5 sums checked

Tests output


Example timings

cn.mops.Rcheck/examples_i386/cn.mops-Ex.timings

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers-CNVDetectionResult-method12.49 0.0312.51
calcFractionalCopyNumbers12.18 0.0012.17
calcIntegerCopyNumbers-CNVDetectionResult-method0.540.020.56
calcIntegerCopyNumbers0.490.000.49
cn.mops 8.81 0.3322.83
cnvr-CNVDetectionResult-method0.360.010.37
cnvr0.360.000.36
cnvs-CNVDetectionResult-method0.290.000.30
cnvs0.300.000.29
exomecn.mops3.690.053.74
getReadCountsFromBAM0.860.017.61
getSegmentReadCountsFromBAM0.480.025.47
gr-CNVDetectionResult-method0.420.020.43
gr0.320.000.32
haplocn.mops 1.50 0.0312.45
individualCall-CNVDetectionResult-method0.370.010.39
individualCall0.330.020.34
iniCall-CNVDetectionResult-method0.30.00.3
iniCall0.310.000.31
integerCopyNumber-CNVDetectionResult-method0.30.00.3
integerCopyNumber0.280.000.28
localAssessments-CNVDetectionResult-method0.280.000.28
localAssessments0.260.010.28
makeRobustCNVR0.490.000.49
normalizeChromosomes0.200.020.22
normalizeGenome0.190.000.19
normalizedData-CNVDetectionResult-method0.250.020.26
normalizedData0.280.000.28
params-CNVDetectionResult-method0.280.000.28
params0.270.000.27
posteriorProbs-CNVDetectionResult-method0.260.000.26
posteriorProbs0.800.010.82
referencecn.mops18.42 0.0230.64
sampleNames-CNVDetectionResult-method0.410.000.40
sampleNames0.330.000.33
segment0.020.000.01
segmentation-CNVDetectionResult-method0.290.000.30
segmentation0.30.00.3
segplot-CNVDetectionResult-method1.060.011.08
segplot1.070.021.07
singlecn.mops0.700.000.71

cn.mops.Rcheck/examples_x64/cn.mops-Ex.timings

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers-CNVDetectionResult-method11.28 0.0211.29
calcFractionalCopyNumbers12.33 0.0812.41
calcIntegerCopyNumbers-CNVDetectionResult-method0.580.010.59
calcIntegerCopyNumbers0.530.000.53
cn.mops 9.08 0.1123.36
cnvr-CNVDetectionResult-method0.440.000.44
cnvr0.430.000.44
cnvs-CNVDetectionResult-method0.440.030.46
cnvs0.440.000.44
exomecn.mops4.550.034.58
getReadCountsFromBAM0.980.007.58
getSegmentReadCountsFromBAM0.530.005.94
gr-CNVDetectionResult-method0.410.020.42
gr0.330.020.34
haplocn.mops 1.46 0.0111.75
individualCall-CNVDetectionResult-method0.350.020.36
individualCall0.290.000.30
iniCall-CNVDetectionResult-method0.320.000.31
iniCall0.280.010.30
integerCopyNumber-CNVDetectionResult-method0.280.000.28
integerCopyNumber0.280.020.30
localAssessments-CNVDetectionResult-method0.300.000.29
localAssessments0.290.010.31
makeRobustCNVR0.540.000.54
normalizeChromosomes0.170.020.18
normalizeGenome0.170.010.19
normalizedData-CNVDetectionResult-method0.300.020.31
normalizedData0.260.020.28
params-CNVDetectionResult-method0.280.000.29
params0.250.010.26
posteriorProbs-CNVDetectionResult-method0.280.000.28
posteriorProbs0.270.000.27
referencecn.mops17.47 0.0028.61
sampleNames-CNVDetectionResult-method0.410.020.42
sampleNames0.310.000.31
segment0.010.000.02
segmentation-CNVDetectionResult-method0.300.000.29
segmentation0.280.000.29
segplot-CNVDetectionResult-method1.130.001.12
segplot1.070.011.09
singlecn.mops0.740.000.74