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This page was generated on 2024-05-04 11:40:23 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 385/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.50.0  (landing page)
Gundula Povysil
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/cn.mops
git_branch: RELEASE_3_19
git_last_commit: 70252ab
git_last_commit_date: 2024-04-30 10:26:19 -0400 (Tue, 30 Apr 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
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.50.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cn.mops_1.50.0.tar.gz
StartedAt: 2024-05-04 06:05:56 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:10:29 -0000 (Sat, 04 May 2024)
EllapsedTime: 272.5 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cn.mops_1.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘1.50.0’
* 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 (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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                                    31.351  0.066  42.088
calcFractionalCopyNumbers-CNVDetectionResult-method 18.204  0.020  18.251
calcFractionalCopyNumbers                           17.967  0.004  18.014
cn.mops                                              8.172  0.098  21.984
haplocn.mops                                         1.487  0.046  12.447
getReadCountsFromBAM                                 0.566  0.006   6.032
getSegmentReadCountsFromBAM                          0.369  0.002   5.892
* 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-3.19-bioc/meat/cn.mops.Rcheck/00check.log’
for details.


Installation output

cn.mops.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include/Rmath.h:210:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
  210 | #define beta  Rf_beta
      |               ^~~~~~~
segment.cpp:64:9: note: in expansion of macro ‘beta’
   64 |  double beta,nn;
      |         ^~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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-method18.204 0.02018.251
calcFractionalCopyNumbers17.967 0.00418.014
calcIntegerCopyNumbers-CNVDetectionResult-method0.5350.0000.536
calcIntegerCopyNumbers0.4860.0000.487
cn.mops 8.172 0.09821.984
cnvr-CNVDetectionResult-method0.2790.0040.284
cnvr0.2880.0000.289
cnvs-CNVDetectionResult-method0.2970.0000.298
cnvs0.2770.0040.283
exomecn.mops3.4760.0203.509
getReadCountsFromBAM0.5660.0066.032
getSegmentReadCountsFromBAM0.3690.0025.892
gr-CNVDetectionResult-method0.2940.0490.346
gr0.2960.0000.298
haplocn.mops 1.487 0.04612.447
individualCall-CNVDetectionResult-method0.3210.0000.321
individualCall0.3090.0000.310
iniCall-CNVDetectionResult-method0.2990.0040.304
iniCall0.2960.0000.297
integerCopyNumber-CNVDetectionResult-method0.2830.0120.295
integerCopyNumber0.3090.0000.310
localAssessments-CNVDetectionResult-method0.3080.0000.309
localAssessments0.2940.0000.294
makeRobustCNVR0.4890.0000.491
normalizeChromosomes0.2390.0160.256
normalizeGenome0.2580.0040.262
normalizedData-CNVDetectionResult-method0.2830.0000.284
normalizedData0.2900.0040.295
params-CNVDetectionResult-method0.2680.0040.272
params0.2880.0000.289
posteriorProbs-CNVDetectionResult-method0.2600.0040.265
posteriorProbs0.2730.0040.278
referencecn.mops31.351 0.06642.088
sampleNames-CNVDetectionResult-method0.2930.0000.293
sampleNames0.2870.0120.300
segment0.0280.0000.028
segmentation-CNVDetectionResult-method0.2930.0000.293
segmentation0.2770.0080.286
segplot-CNVDetectionResult-method1.3190.0081.330
segplot1.3180.0041.325
singlecn.mops0.9540.0080.964