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This page was generated on 2021-11-26 15:04:48 -0500 (Fri, 26 Nov 2021).

CHECK results for cn.mops on nebbiolo2

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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 348/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.40.0  (landing page)
Gundula Povysil
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_14
git_last_commit: 498dbf7
git_last_commit_date: 2021-10-26 12:01:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 1.40.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cn.mops_1.40.0.tar.gz
StartedAt: 2021-11-25 08:51:28 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 08:54:42 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 193.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cn.mops_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/cn.mops.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.40.0’
* 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                                    6.900  0.008  16.457
cn.mops                                             6.302  0.567  18.677
calcFractionalCopyNumbers-CNVDetectionResult-method 5.589  0.047   5.636
calcFractionalCopyNumbers                           5.405  0.032   5.437
haplocn.mops                                        1.188  0.014  10.370
* 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-3.14-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-3.14-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-bioc/R/include/Rmath.h:208:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  208 | #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-3.14-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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
CNVDetectionResult0.0010.0000.002
calcFractionalCopyNumbers-CNVDetectionResult-method5.5890.0475.636
calcFractionalCopyNumbers5.4050.0325.437
calcIntegerCopyNumbers-CNVDetectionResult-method0.8580.0080.867
calcIntegerCopyNumbers0.5050.0040.510
cn.mops 6.302 0.56718.677
cnvr-CNVDetectionResult-method0.2160.0320.248
cnvr0.2600.0040.264
cnvs-CNVDetectionResult-method0.2460.0000.246
cnvs0.2380.0040.243
exomecn.mops2.1820.0362.218
getReadCountsFromBAM0.5060.0174.634
getSegmentReadCountsFromBAM0.3110.0074.695
gr-CNVDetectionResult-method0.3990.0120.411
gr0.3690.0040.373
haplocn.mops 1.188 0.01410.370
individualCall-CNVDetectionResult-method0.2920.0080.300
individualCall0.6990.0800.779
iniCall-CNVDetectionResult-method0.2540.0000.254
iniCall0.2380.0040.243
integerCopyNumber-CNVDetectionResult-method0.2550.0080.263
integerCopyNumber0.2650.0000.265
localAssessments-CNVDetectionResult-method0.2530.0000.253
localAssessments0.2620.0080.270
makeRobustCNVR0.490.000.49
normalizeChromosomes0.1650.0080.174
normalizeGenome0.1480.0200.168
normalizedData-CNVDetectionResult-method0.2710.0000.271
normalizedData0.2500.0040.253
params-CNVDetectionResult-method0.2360.0140.250
params0.2910.0010.293
posteriorProbs-CNVDetectionResult-method0.3270.0000.327
posteriorProbs0.3350.0080.343
referencecn.mops 6.900 0.00816.457
sampleNames-CNVDetectionResult-method0.2640.0000.264
sampleNames0.2080.0080.216
segment0.0170.0000.018
segmentation-CNVDetectionResult-method0.2380.0000.239
segmentation0.2480.0000.247
segplot-CNVDetectionResult-method0.8850.0040.889
segplot0.9110.0000.911
singlecn.mops0.6520.0080.659