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This page was generated on 2021-09-20 15:04:46 -0400 (Mon, 20 Sep 2021).

CHECK results for cn.mops on nebbiolo1

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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: 2021-09-19 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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cn.mops_1.38.0.tar.gz
StartedAt: 2021-09-19 09:16:36 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:19:35 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 178.9 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cn.mops_1.38.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cn.mops.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    6.984  0.017  16.455
calcFractionalCopyNumbers-CNVDetectionResult-method 5.493  0.271   5.765
cn.mops                                             5.416  0.184  16.694
calcFractionalCopyNumbers                           4.992  0.072   5.064
haplocn.mops                                        1.187  0.008  10.634
getReadCountsFromBAM                                0.529  0.015   5.094
* 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
  ‘/home/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:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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:
/home/biocbuild/bbs-3.13-bioc/R/include/Rmath.h:212:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  212 | #define beta  Rf_beta
      |               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro ‘beta’
   64 |  double beta,nn;
      |         ^~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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
CNVDetectionResult0.0020.0000.002
calcFractionalCopyNumbers-CNVDetectionResult-method5.4930.2715.765
calcFractionalCopyNumbers4.9920.0725.064
calcIntegerCopyNumbers-CNVDetectionResult-method0.5480.0040.552
calcIntegerCopyNumbers0.4860.0000.486
cn.mops 5.416 0.18416.694
cnvr-CNVDetectionResult-method0.2320.0000.232
cnvr0.2380.0000.238
cnvs-CNVDetectionResult-method0.2270.0070.235
cnvs0.2300.0050.234
exomecn.mops2.1650.0112.178
getReadCountsFromBAM0.5290.0155.094
getSegmentReadCountsFromBAM0.3260.0004.802
gr-CNVDetectionResult-method0.3220.0000.322
gr0.2500.0080.258
haplocn.mops 1.187 0.00810.634
individualCall-CNVDetectionResult-method0.250.000.25
individualCall0.2660.0000.265
iniCall-CNVDetectionResult-method0.6560.0000.656
iniCall0.2460.0040.249
integerCopyNumber-CNVDetectionResult-method0.2420.0040.245
integerCopyNumber0.2470.0040.251
localAssessments-CNVDetectionResult-method0.2400.0040.244
localAssessments0.2370.0080.244
makeRobustCNVR0.4810.0040.485
normalizeChromosomes0.1550.0040.159
normalizeGenome0.1690.0040.174
normalizedData-CNVDetectionResult-method0.2820.0000.282
normalizedData0.2730.0000.273
params-CNVDetectionResult-method0.2650.0200.285
params0.2470.0120.260
posteriorProbs-CNVDetectionResult-method0.2290.0000.228
posteriorProbs0.2220.0040.226
referencecn.mops 6.984 0.01716.455
sampleNames-CNVDetectionResult-method0.2410.0080.249
sampleNames0.2520.0040.256
segment0.0340.0000.035
segmentation-CNVDetectionResult-method0.2430.0040.246
segmentation0.2310.0040.235
segplot-CNVDetectionResult-method0.8970.0000.897
segplot0.9260.0000.926
singlecn.mops0.6050.0000.606