Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-25 12:07 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 394/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.55.1  (landing page)
Gundula Povysil
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 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 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cn.mops on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cn.mops
Version: 1.55.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cn.mops_1.55.1.tar.gz
StartedAt: 2025-09-23 05:59:51 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 06:04:09 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 258.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cn.mops_1.55.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cn.mops.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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                                    28.603  0.027  38.859
calcFractionalCopyNumbers-CNVDetectionResult-method 16.976  0.028  17.022
calcFractionalCopyNumbers                           16.757  0.000  16.792
cn.mops                                              7.884  0.098  21.456
haplocn.mops                                         1.444  0.021  12.294
getReadCountsFromBAM                                 0.599  0.012   5.903
getSegmentReadCountsFromBAM                          0.374  0.000   5.765
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cn.mops.Rcheck/00check.log’
for details.


Installation output

cn.mops.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘cn.mops’ ...
** this is package ‘cn.mops’ version ‘1.55.1’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c R_init_cnmops.c -o R_init_cnmops.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c cnmops.cpp -o cnmops.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/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;
      |                ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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-method16.976 0.02817.022
calcFractionalCopyNumbers16.757 0.00016.792
calcIntegerCopyNumbers-CNVDetectionResult-method0.5500.0000.552
calcIntegerCopyNumbers0.5340.0000.536
cn.mops 7.884 0.09821.456
cnvr-CNVDetectionResult-method0.3360.0440.381
cnvr0.2870.0080.295
cnvs-CNVDetectionResult-method0.3060.0470.355
cnvs0.2870.0390.328
exomecn.mops3.5520.1163.681
getReadCountsFromBAM0.5990.0125.903
getSegmentReadCountsFromBAM0.3740.0005.765
gr-CNVDetectionResult-method0.3030.0040.308
gr0.280.020.30
haplocn.mops 1.444 0.02112.294
individualCall-CNVDetectionResult-method0.2830.0000.284
individualCall0.3010.0000.301
iniCall-CNVDetectionResult-method0.2950.0000.296
iniCall0.2790.0000.280
integerCopyNumber-CNVDetectionResult-method0.2900.0000.292
integerCopyNumber0.2890.0000.291
localAssessments-CNVDetectionResult-method0.2780.0040.282
localAssessments0.5840.1670.754
makeRobustCNVR0.4920.0000.493
normalizeChromosomes0.2060.0120.218
normalizeGenome0.2140.0040.219
normalizedData-CNVDetectionResult-method0.2760.0000.277
normalizedData0.2880.0040.292
params-CNVDetectionResult-method0.2630.0080.272
params0.2660.0080.276
posteriorProbs-CNVDetectionResult-method0.2670.0040.272
posteriorProbs0.2640.0000.265
referencecn.mops28.603 0.02738.859
sampleNames-CNVDetectionResult-method0.2610.0000.262
sampleNames0.2720.0000.273
segment0.0270.0000.027
segmentation-CNVDetectionResult-method0.2640.0040.269
segmentation0.2680.0040.274
segplot-CNVDetectionResult-method1.2050.0001.210
segplot1.2020.0041.210
singlecn.mops0.9130.0040.920