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This page was generated on 2024-05-04 11:39:00 -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 lconway


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: 1.50.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.50.0.tar.gz
StartedAt: 2024-05-03 20:56:29 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:00:10 -0400 (Fri, 03 May 2024)
EllapsedTime: 220.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    7.230  0.102  17.951
calcFractionalCopyNumbers-CNVDetectionResult-method 6.427  0.094   6.629
cn.mops                                             6.264  0.198  19.814
calcFractionalCopyNumbers                           5.990  0.069   6.159
haplocn.mops                                        1.126  0.044  11.688
getReadCountsFromBAM                                0.471  0.022   5.886
getSegmentReadCountsFromBAM                         0.311  0.017   5.953
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck/00check.log’
for details.


Installation output

cn.mops.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cnmops.cpp -o cnmops.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c segment.cpp -o segment.o
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
        double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                                     ^
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
        double globalMean,globalSd,diff,M2,globalVariance;
                          ^
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
        double beta,nn;
               ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta'
#define beta            Rf_beta
                        ^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
        double oldStatistic, meanLeft,meanRight,varLeft,varRight;
               ^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
        double newPValue, maxPValue,oldPValue,maxIdx;
                                              ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
CNVDetectionResult0.0010.0010.004
calcFractionalCopyNumbers-CNVDetectionResult-method6.4270.0946.629
calcFractionalCopyNumbers5.9900.0696.159
calcIntegerCopyNumbers-CNVDetectionResult-method0.4870.0090.499
calcIntegerCopyNumbers0.4180.0080.429
cn.mops 6.264 0.19819.814
cnvr-CNVDetectionResult-method0.2380.0080.246
cnvr0.5560.0150.576
cnvs-CNVDetectionResult-method0.2270.0060.235
cnvs0.2020.0040.210
exomecn.mops2.6870.0472.788
getReadCountsFromBAM0.4710.0225.886
getSegmentReadCountsFromBAM0.3110.0175.953
gr-CNVDetectionResult-method0.2380.0050.247
gr0.2380.0060.248
haplocn.mops 1.126 0.04411.688
individualCall-CNVDetectionResult-method0.2420.0060.254
individualCall0.2650.0070.275
iniCall-CNVDetectionResult-method0.2590.0060.273
iniCall0.2530.0050.261
integerCopyNumber-CNVDetectionResult-method0.2580.0050.266
integerCopyNumber0.2310.0040.236
localAssessments-CNVDetectionResult-method0.2770.0070.287
localAssessments0.2580.0060.265
makeRobustCNVR0.7280.0080.743
normalizeChromosomes0.1340.0070.142
normalizeGenome0.1550.0170.173
normalizedData-CNVDetectionResult-method0.2470.0060.255
normalizedData0.2660.0100.280
params-CNVDetectionResult-method0.2420.0120.255
params0.2280.0120.242
posteriorProbs-CNVDetectionResult-method0.2490.0050.256
posteriorProbs0.2280.0030.235
referencecn.mops 7.230 0.10217.951
sampleNames-CNVDetectionResult-method0.2430.0050.251
sampleNames0.2280.0060.236
segment0.0240.0000.025
segmentation-CNVDetectionResult-method0.2480.0040.256
segmentation0.2310.0030.238
segplot-CNVDetectionResult-method1.0830.0181.114
segplot1.1080.0141.145
singlecn.mops0.7160.0100.734