Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 386/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.52.0  (landing page)
Gundula Povysil
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_20
git_last_commit: 3a21e19
git_last_commit_date: 2024-10-29 09:39:23 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for cn.mops on kunpeng2

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: 1.52.0
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_1.52.0.tar.gz
StartedAt: 2024-11-20 06:23:43 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:28:27 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 283.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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### 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_1.52.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cn.mops.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 ‘1.52.0’
* 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 (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 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                                    31.977  0.036  43.565
calcFractionalCopyNumbers-CNVDetectionResult-method 18.742  0.048  18.817
calcFractionalCopyNumbers                           18.529  0.052  18.603
cn.mops                                              8.670  0.101  22.344
haplocn.mops                                         1.434  0.056  12.821
getReadCountsFromBAM                                 0.614  0.014   6.703
getSegmentReadCountsFromBAM                          0.404  0.019   6.040
* 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-3.20-bioc/meat/cn.mops.Rcheck/00check.log’
for details.


Installation output

cn.mops.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cnmops.cpp -o cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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-method18.742 0.04818.817
calcFractionalCopyNumbers18.529 0.05218.603
calcIntegerCopyNumbers-CNVDetectionResult-method0.5480.0040.553
calcIntegerCopyNumbers0.4560.0080.466
cn.mops 8.670 0.10122.344
cnvr-CNVDetectionResult-method0.3050.0160.321
cnvr0.2880.0110.300
cnvs-CNVDetectionResult-method0.2770.0120.290
cnvs0.2740.0080.282
exomecn.mops3.7570.1123.711
getReadCountsFromBAM0.6140.0146.703
getSegmentReadCountsFromBAM0.4040.0196.040
gr-CNVDetectionResult-method0.2740.0120.286
gr0.2940.0160.310
haplocn.mops 1.434 0.05612.821
individualCall-CNVDetectionResult-method0.3150.0240.339
individualCall0.3070.0160.324
iniCall-CNVDetectionResult-method0.2920.0120.305
iniCall0.2890.0040.295
integerCopyNumber-CNVDetectionResult-method0.2800.0080.288
integerCopyNumber0.2990.0160.315
localAssessments-CNVDetectionResult-method0.2930.0000.293
localAssessments0.2830.0080.292
makeRobustCNVR0.5020.0120.516
normalizeChromosomes0.3290.0360.265
normalizeGenome0.4020.0080.248
normalizedData-CNVDetectionResult-method0.3600.0040.295
normalizedData0.2960.0160.313
params-CNVDetectionResult-method0.2730.0040.278
params0.7050.0320.738
posteriorProbs-CNVDetectionResult-method0.2610.0040.266
posteriorProbs0.2760.0040.281
referencecn.mops31.977 0.03643.565
sampleNames-CNVDetectionResult-method0.2800.0230.305
sampleNames0.2610.0160.278
segment0.0260.0000.026
segmentation-CNVDetectionResult-method0.2820.0040.289
segmentation0.2880.0040.292
segplot-CNVDetectionResult-method1.2730.0201.296
segplot1.2850.0121.302
singlecn.mops0.9440.0320.979