Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:04 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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

Package 390/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.55.1  (landing page)
Gundula Povysil
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: devel
git_last_commit: 8f56f3e
git_last_commit_date: 2025-07-22 22:34:45 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for cn.mops on nebbiolo2

To the developers/maintainers of the cn.mops package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cn.mops
Version: 1.55.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cn.mops_1.55.1.tar.gz
StartedAt: 2025-08-08 21:08:08 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:11:21 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 193.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cn.mops_1.55.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cn.mops.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.55.1’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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                                    8.431  0.023  16.729
calcFractionalCopyNumbers-CNVDetectionResult-method 5.959  0.023   5.981
calcFractionalCopyNumbers                           5.804  0.006   5.810
cn.mops                                             5.203  0.058  15.131
haplocn.mops                                        1.016  0.129   9.601
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-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-3.22-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘cn.mops’ ...
** this is package ‘cn.mops’ version ‘1.55.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c cnmops.cpp -o cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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-3.22-bioc/R/include/Rmath.h:221:25: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  221 | #define beta            Rf_beta
      |                         ^~~~~~~
segment.cpp:64:16: note: in expansion of macro ‘beta’
   64 |         double beta,nn;
      |                ^~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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
CNVDetectionResult0.0010.0000.001
calcFractionalCopyNumbers-CNVDetectionResult-method5.9590.0235.981
calcFractionalCopyNumbers5.8040.0065.810
calcIntegerCopyNumbers-CNVDetectionResult-method0.3790.0030.381
calcIntegerCopyNumbers0.3900.0010.392
cn.mops 5.203 0.05815.131
cnvr-CNVDetectionResult-method0.2160.0010.217
cnvr0.1930.0030.196
cnvs-CNVDetectionResult-method0.2040.0000.204
cnvs0.1910.0020.193
exomecn.mops2.1140.0082.122
getReadCountsFromBAM0.4090.0044.607
getSegmentReadCountsFromBAM0.2840.0034.625
gr-CNVDetectionResult-method0.2610.0950.355
gr0.2320.0510.283
haplocn.mops1.0160.1299.601
individualCall-CNVDetectionResult-method0.2140.0190.234
individualCall0.2150.0040.220
iniCall-CNVDetectionResult-method0.2180.0040.223
iniCall0.2100.0040.214
integerCopyNumber-CNVDetectionResult-method0.2340.0080.242
integerCopyNumber0.2090.0080.217
localAssessments-CNVDetectionResult-method0.2000.0050.205
localAssessments0.5220.2150.737
makeRobustCNVR0.3590.0080.367
normalizeChromosomes0.1370.0200.156
normalizeGenome0.1480.0160.164
normalizedData-CNVDetectionResult-method0.2010.0040.206
normalizedData0.2120.0030.215
params-CNVDetectionResult-method0.1930.0050.197
params0.2000.0040.204
posteriorProbs-CNVDetectionResult-method0.2040.0010.204
posteriorProbs0.1910.0020.192
referencecn.mops 8.431 0.02316.729
sampleNames-CNVDetectionResult-method0.1940.0000.195
sampleNames0.1990.0010.200
segment0.0180.0000.018
segmentation-CNVDetectionResult-method0.1990.0020.201
segmentation0.2140.0000.214
segplot-CNVDetectionResult-method0.8400.0010.841
segplot0.8550.0080.863
singlecn.mops0.6190.0040.623