Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-18 11:05:27 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 nebbiolo1


To the developers/maintainers of the cn.mops package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 345/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.41.1  (landing page)
Gundula Povysil
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: master
git_last_commit: cd0cc29
git_last_commit_date: 2021-11-20 03:52:29 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.mops
Version: 1.41.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings cn.mops_1.41.1.tar.gz
StartedAt: 2022-01-17 18:36:42 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 18:39:32 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 169.7 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings cn.mops_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.41.1’
* 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
* 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 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                                    6.771  0.010  15.994
calcFractionalCopyNumbers-CNVDetectionResult-method 5.614  0.056   5.671
cn.mops                                             5.295  0.031  16.161
haplocn.mops                                        0.945  0.006  10.293
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.15-bioc/meat/cn.mops.Rcheck/00check.log’
for details.



Installation output

cn.mops.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-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:59:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
   59 |  double globalMean,globalSd,diff,M2,globalVariance;
      |                    ^~~~~~~~
segment.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
   60 |  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
      |         ^~~~~~~~~~~~
segment.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
   61 |  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
      |                               ^~~~~~~~~~~~
segment.cpp:62:40: 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-3.15-bioc/R/include/Rmath.h:209:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  209 | #define beta  Rf_beta
      |               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro ‘beta’
   64 |  double beta,nn;
      |         ^~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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
CNVDetectionResult0.0000.0010.002
calcFractionalCopyNumbers-CNVDetectionResult-method5.6140.0565.671
calcFractionalCopyNumbers4.8490.0204.869
calcIntegerCopyNumbers-CNVDetectionResult-method0.4680.0000.468
calcIntegerCopyNumbers0.380.000.38
cn.mops 5.295 0.03116.161
cnvr-CNVDetectionResult-method0.1850.0040.188
cnvr0.1960.0190.215
cnvs-CNVDetectionResult-method0.1960.0200.217
cnvs0.1850.0000.185
exomecn.mops1.9820.0121.994
getReadCountsFromBAM0.5280.0054.919
getSegmentReadCountsFromBAM0.2400.0094.731
gr-CNVDetectionResult-method0.2130.0040.217
gr0.1930.0000.193
haplocn.mops 0.945 0.00610.293
individualCall-CNVDetectionResult-method0.2220.0070.229
individualCall0.2300.0040.234
iniCall-CNVDetectionResult-method0.2150.0040.218
iniCall0.2060.0040.209
integerCopyNumber-CNVDetectionResult-method0.2330.0040.238
integerCopyNumber0.2030.0030.205
localAssessments-CNVDetectionResult-method0.1970.0120.209
localAssessments0.2180.0040.222
makeRobustCNVR0.4120.0040.416
normalizeChromosomes0.1590.0040.163
normalizeGenome0.5170.0000.517
normalizedData-CNVDetectionResult-method0.2340.0040.238
normalizedData0.1970.0000.198
params-CNVDetectionResult-method0.2700.0120.282
params0.2110.0200.231
posteriorProbs-CNVDetectionResult-method0.210.000.21
posteriorProbs0.2140.0040.218
referencecn.mops 6.771 0.01015.994
sampleNames-CNVDetectionResult-method0.1720.0040.177
sampleNames0.1740.0000.174
segment0.0160.0000.015
segmentation-CNVDetectionResult-method0.1790.0040.183
segmentation0.1760.0080.183
segplot-CNVDetectionResult-method0.7260.0040.730
segplot0.7580.0040.762
singlecn.mops0.5510.0080.559