Build/check report for BioC 3.22 - CHECK results for cn.mops on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.55.1.tar.gz

StartedAt: 2025-10-26 19:12:58 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 19:13:59 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 61.7 seconds

RetCode: 0

Status: OK

CheckDir: cn.mops.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.55.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cn.mops.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 ‘1.55.1’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
referencecn.mops 2.935  0.015   5.770
cn.mops          1.489  0.046   5.084
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.mops
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘cn.mops’ ...
** this is package ‘cn.mops’ version ‘1.55.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cnmops.cpp -o cnmops.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c segment.cpp -o segment.o
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
        double globalMean,globalSd,diff,M2,globalVariance;
                          ^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
        double oldStatistic, meanLeft,meanRight,varLeft,varRight;
               ^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
        double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                                     ^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
        double newPValue, maxPValue,oldPValue,maxIdx;
                                              ^
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
        double beta,nn;
               ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:221:15: note: expanded from macro 'beta'
#define beta            Rf_beta
                        ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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

name	user	system	elapsed
CNVDetectionResult	0.000	0.001	0.001
calcFractionalCopyNumbers-CNVDetectionResult-method	2.051	0.014	2.066
calcFractionalCopyNumbers	2.016	0.009	2.025
calcIntegerCopyNumbers-CNVDetectionResult-method	0.121	0.002	0.121
calcIntegerCopyNumbers	0.269	0.001	0.270
cn.mops	1.489	0.046	5.084
cnvr-CNVDetectionResult-method	0.062	0.002	0.064
cnvr	0.062	0.001	0.064
cnvs-CNVDetectionResult-method	0.063	0.001	0.064
cnvs	0.064	0.002	0.064
exomecn.mops	0.662	0.007	0.670
getReadCountsFromBAM	0.124	0.007	1.668
getSegmentReadCountsFromBAM	0.076	0.006	1.646
gr-CNVDetectionResult-method	0.068	0.001	0.069
gr	0.065	0.001	0.066
haplocn.mops	0.287	0.012	3.252
individualCall-CNVDetectionResult-method	0.066	0.001	0.067
individualCall	0.068	0.001	0.069
iniCall-CNVDetectionResult-method	0.072	0.001	0.073
iniCall	0.069	0.001	0.069
integerCopyNumber-CNVDetectionResult-method	0.065	0.001	0.066
integerCopyNumber	0.066	0.002	0.067
localAssessments-CNVDetectionResult-method	0.062	0.001	0.062
localAssessments	0.059	0.001	0.060
makeRobustCNVR	0.220	0.004	0.224
normalizeChromosomes	0.047	0.003	0.050
normalizeGenome	0.050	0.004	0.054
normalizedData-CNVDetectionResult-method	0.058	0.001	0.059
normalizedData	0.060	0.002	0.063
params-CNVDetectionResult-method	0.056	0.003	0.059
params	0.057	0.004	0.061
posteriorProbs-CNVDetectionResult-method	0.057	0.001	0.058
posteriorProbs	0.055	0.002	0.056
referencecn.mops	2.935	0.015	5.770
sampleNames-CNVDetectionResult-method	0.062	0.002	0.063
sampleNames	0.064	0.001	0.066
segment	0.006	0.000	0.006
segmentation-CNVDetectionResult-method	0.064	0.002	0.065
segmentation	0.067	0.001	0.068
segplot-CNVDetectionResult-method	0.248	0.002	0.251
segplot	0.253	0.002	0.256
singlecn.mops	0.224	0.004	0.228