Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-02-01 11:05:18 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 355/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.45.0  (landing page)
Gundula Povysil
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: master
git_last_commit: 0617906
git_last_commit_date: 2022-11-01 11:06:31 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.45.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cn.mops_1.45.0.tar.gz
StartedAt: 2023-01-31 19:41:42 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 19:45:20 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 218.0 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cn.mops_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.45.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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                                    6.818  0.040  15.943
calcFractionalCopyNumbers-CNVDetectionResult-method 5.146  0.052   5.198
cn.mops                                             5.010  0.096  16.630
calcFractionalCopyNumbers                           5.001  0.027   5.029
haplocn.mops                                        1.011  0.021  10.866
getReadCountsFromBAM                                0.426  0.032   5.018
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cn.mops.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-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-3.17-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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:59:27: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
   59 |         double globalMean,globalSd,diff,M2,globalVariance;
      |                           ^~~~~~~~
segment.cpp:60:16: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
   60 |         double oldStatistic, meanLeft,meanRight,varLeft,varRight;
      |                ^~~~~~~~~~~~
segment.cpp:61:38: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
   61 |         double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
      |                                      ^~~~~~~~~~~~
segment.cpp:62:47: 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-3.17-bioc/R/include/Rmath.h:210:25: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  210 | #define beta            Rf_beta
      |                         ^~~~~~~
segment.cpp:64:16: note: in expansion of macro ‘beta’
   64 |         double beta,nn;
      |                ^~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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
CNVDetectionResult0.0010.0010.001
calcFractionalCopyNumbers-CNVDetectionResult-method5.1460.0525.198
calcFractionalCopyNumbers5.0010.0275.029
calcIntegerCopyNumbers-CNVDetectionResult-method0.4280.0080.437
calcIntegerCopyNumbers0.360.000.36
cn.mops 5.010 0.09616.630
cnvr-CNVDetectionResult-method0.2250.0160.242
cnvr0.6810.2840.965
cnvs-CNVDetectionResult-method0.2080.0080.216
cnvs0.2060.0000.206
exomecn.mops2.1880.1602.348
getReadCountsFromBAM0.4260.0325.018
getSegmentReadCountsFromBAM0.280.044.98
gr-CNVDetectionResult-method0.2350.0040.239
gr0.2130.0200.234
haplocn.mops 1.011 0.02110.866
individualCall-CNVDetectionResult-method0.2250.0240.249
individualCall0.2360.0040.240
iniCall-CNVDetectionResult-method0.2190.0040.223
iniCall0.2070.0000.207
integerCopyNumber-CNVDetectionResult-method0.2130.0070.221
integerCopyNumber0.2050.0040.209
localAssessments-CNVDetectionResult-method0.2230.0000.223
localAssessments0.2240.0000.224
makeRobustCNVR0.3650.0040.369
normalizeChromosomes0.1470.0120.158
normalizeGenome0.5400.0520.593
normalizedData-CNVDetectionResult-method0.2060.0040.210
normalizedData0.2180.0000.218
params-CNVDetectionResult-method0.2000.0110.211
params0.1970.0180.215
posteriorProbs-CNVDetectionResult-method0.1880.0010.189
posteriorProbs0.1960.0000.196
referencecn.mops 6.818 0.04015.943
sampleNames-CNVDetectionResult-method0.2080.0320.240
sampleNames0.2190.0190.238
segment0.0190.0000.019
segmentation-CNVDetectionResult-method0.2310.0000.231
segmentation0.2160.0120.228
segplot-CNVDetectionResult-method0.9130.0080.921
segplot0.8720.0000.871
singlecn.mops0.6120.0040.616