Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-23 12:05:04 -0400 (Mon, 23 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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: 2022-05-22 13:55:15 -0400 (Sun, 22 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings cn.mops_1.42.0.tar.gz
StartedAt: 2022-05-22 18:56:38 -0400 (Sun, 22 May 2022)
EndedAt: 2022-05-22 18:59:30 -0400 (Sun, 22 May 2022)
EllapsedTime: 172.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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                                    6.616  0.024  15.482
calcFractionalCopyNumbers-CNVDetectionResult-method 5.643  0.011   5.655
cn.mops                                             5.076  0.038  16.378
haplocn.mops                                        0.976  0.010  10.196
* 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-3.15-bioc/meat/cn.mops.Rcheck/00check.log’
for details.



Installation output

cn.mops.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-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-3.15-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-3.15-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++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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-method5.6430.0115.655
calcFractionalCopyNumbers4.9140.0674.982
calcIntegerCopyNumbers-CNVDetectionResult-method0.3850.0040.389
calcIntegerCopyNumbers0.3500.0110.361
cn.mops 5.076 0.03816.378
cnvr-CNVDetectionResult-method0.5880.0560.645
cnvr0.2010.0040.205
cnvs-CNVDetectionResult-method0.2130.0000.213
cnvs0.2120.0040.216
exomecn.mops2.3930.0282.421
getReadCountsFromBAM0.4650.0044.861
getSegmentReadCountsFromBAM0.2420.0064.540
gr-CNVDetectionResult-method0.2110.0040.215
gr0.2090.0040.213
haplocn.mops 0.976 0.01010.196
individualCall-CNVDetectionResult-method0.2070.0040.211
individualCall0.2010.0040.205
iniCall-CNVDetectionResult-method0.2030.0040.206
iniCall0.220.000.22
integerCopyNumber-CNVDetectionResult-method0.1880.0080.196
integerCopyNumber0.1950.0040.200
localAssessments-CNVDetectionResult-method0.1950.0040.198
localAssessments0.1990.0000.199
makeRobustCNVR0.3520.0000.352
normalizeChromosomes0.5750.0040.579
normalizeGenome0.1390.0040.144
normalizedData-CNVDetectionResult-method0.2000.0040.204
normalizedData0.2130.0000.214
params-CNVDetectionResult-method0.2140.0160.230
params0.1820.0200.202
posteriorProbs-CNVDetectionResult-method0.1820.0000.183
posteriorProbs0.1820.0080.190
referencecn.mops 6.616 0.02415.482
sampleNames-CNVDetectionResult-method0.1800.0040.185
sampleNames0.1740.0070.181
segment0.0170.0000.017
segmentation-CNVDetectionResult-method0.1940.0080.201
segmentation0.190.000.19
segplot-CNVDetectionResult-method0.7730.0040.778
segplot0.8220.0040.827
singlecn.mops0.6020.0000.602