Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-22 12:48:04 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 380/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.49.0  (landing page)
Gundula Povysil
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: devel
git_last_commit: e309333
git_last_commit_date: 2024-01-19 07:20:54 -0500 (Fri, 19 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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

CHECK results for cn.mops on nebbiolo1


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: 1.49.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cn.mops_1.49.0.tar.gz
StartedAt: 2024-02-21 21:38:32 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 21:41:55 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 203.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cn.mops_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.49.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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                                    6.796  0.094  16.507
cn.mops                                             5.376  0.059  16.555
calcFractionalCopyNumbers-CNVDetectionResult-method 5.162  0.036   5.199
calcFractionalCopyNumbers                           5.109  0.024   5.133
haplocn.mops                                        0.961  0.013  10.279
getReadCountsFromBAM                                0.492  0.004   5.367
getSegmentReadCountsFromBAM                         0.280  0.001   5.401
* 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-3.19-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-3.19-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-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++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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-3.19-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++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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-method5.1620.0365.199
calcFractionalCopyNumbers5.1090.0245.133
calcIntegerCopyNumbers-CNVDetectionResult-method0.3740.0030.378
calcIntegerCopyNumbers0.3690.0000.369
cn.mops 5.376 0.05916.555
cnvr-CNVDetectionResult-method0.1980.0080.207
cnvr0.1930.0080.202
cnvs-CNVDetectionResult-method0.1950.0080.204
cnvs0.1800.0110.193
exomecn.mops2.1620.0162.179
getReadCountsFromBAM0.4920.0045.367
getSegmentReadCountsFromBAM0.2800.0015.401
gr-CNVDetectionResult-method0.2050.0080.213
gr0.1950.0080.203
haplocn.mops 0.961 0.01310.279
individualCall-CNVDetectionResult-method0.2010.0040.205
individualCall0.2040.0080.212
iniCall-CNVDetectionResult-method0.2000.0000.199
iniCall0.2000.0080.208
integerCopyNumber-CNVDetectionResult-method0.2080.0040.211
integerCopyNumber0.5590.0040.563
localAssessments-CNVDetectionResult-method0.2090.0080.216
localAssessments0.2160.0000.217
makeRobustCNVR0.3550.0040.360
normalizeChromosomes0.150.000.15
normalizeGenome0.1360.0080.143
normalizedData-CNVDetectionResult-method0.2260.0040.230
normalizedData0.2440.0040.248
params-CNVDetectionResult-method0.2050.0120.218
params0.1950.0200.215
posteriorProbs-CNVDetectionResult-method0.1860.0040.190
posteriorProbs0.1980.0000.198
referencecn.mops 6.796 0.09416.507
sampleNames-CNVDetectionResult-method0.2060.1240.330
sampleNames0.2310.0800.310
segment0.0200.0000.019
segmentation-CNVDetectionResult-method0.2100.0040.214
segmentation0.2150.0080.224
segplot-CNVDetectionResult-method0.8580.0240.883
segplot0.8730.0200.893
singlecn.mops0.6090.0320.641