Gundula Povysil
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Sat, 20 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:13 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 346/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.mops 1.41.1 (landing page) Gundula Povysil
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: cn.mops |
| Version: 1.41.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cn.mops_1.41.1.tar.gz |
| StartedAt: 2022-03-17 18:45:18 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:48:35 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 197.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cn.mops_1.41.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/cn.mops/libs/x64/cn.mops.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
referencecn.mops 14.15 0.00 23.13
calcFractionalCopyNumbers-CNVDetectionResult-method 8.18 0.02 8.21
cn.mops 8.09 0.11 21.67
calcFractionalCopyNumbers 7.96 0.11 8.07
haplocn.mops 1.00 0.02 9.47
getReadCountsFromBAM 0.52 0.02 5.04
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/cn.mops.Rcheck/00check.log'
for details.
cn.mops.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cn.mops
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cn.mops' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
double globalMean,globalSd,diff,M2,globalVariance;
^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^~~~~~~~~~~~
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:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^~~~~~
In file included from segment.cpp:10:
D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:209:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
#define beta Rf_beta
^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
double beta,nn;
^~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-cn.mops/00new/cn.mops/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.mops'
finding HTML links ... done
CNVDetectionResult html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-cn.mops/00new/cn.mops/help/cnvdetectionresult.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-cn.mops/00new/cn.mops/help/CnvDetectionResult.html
CNVRanges html
X html
XRanges html
calcFractionalCopyNumbers-CNVDetectionResult-method
html
calcFractionalCopyNumbers html
calcIntegerCopyNumbers-CNVDetectionResult-method
html
calcIntegerCopyNumbers html
cn.mops html
cnvr-CNVDetectionResult-method html
cnvr html
cnvs-CNVDetectionResult-method html
cnvs html
exomeCounts html
exomecn.mops html
getReadCountsFromBAM html
getSegmentReadCountsFromBAM html
gr-CNVDetectionResult-method html
gr html
haplocn.mops html
individualCall-CNVDetectionResult-method
html
individualCall html
iniCall-CNVDetectionResult-method html
iniCall html
integerCopyNumber-CNVDetectionResult-method
html
integerCopyNumber html
localAssessments-CNVDetectionResult-method
html
localAssessments html
makeRobustCNVR html
normalizeChromosomes html
normalizeGenome html
normalizedData-CNVDetectionResult-method
html
normalizedData html
params-CNVDetectionResult-method html
params html
plot html
posteriorProbs-CNVDetectionResult-method
html
posteriorProbs html
referencecn.mops html
sampleNames-CNVDetectionResult-method html
sampleNames html
segment html
segmentation-CNVDetectionResult-method
html
segmentation html
segplot-CNVDetectionResult-method html
segplot html
show html
singlecn.mops html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cn.mops)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'powerTCR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'semisup' is missing or broken
done
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0 | 0 | 0 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 8.18 | 0.02 | 8.21 | |
| calcFractionalCopyNumbers | 7.96 | 0.11 | 8.07 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.30 | 0.03 | 0.33 | |
| calcIntegerCopyNumbers | 0.33 | 0.03 | 0.36 | |
| cn.mops | 8.09 | 0.11 | 21.67 | |
| cnvr-CNVDetectionResult-method | 0.16 | 0.01 | 0.18 | |
| cnvr | 0.19 | 0.00 | 0.18 | |
| cnvs-CNVDetectionResult-method | 0.28 | 0.02 | 0.30 | |
| cnvs | 0.23 | 0.00 | 0.23 | |
| exomecn.mops | 3.14 | 0.06 | 3.21 | |
| getReadCountsFromBAM | 0.52 | 0.02 | 5.04 | |
| getSegmentReadCountsFromBAM | 0.30 | 0.00 | 4.47 | |
| gr-CNVDetectionResult-method | 0.15 | 0.01 | 0.18 | |
| gr | 0.17 | 0.03 | 0.20 | |
| haplocn.mops | 1.00 | 0.02 | 9.47 | |
| individualCall-CNVDetectionResult-method | 0.19 | 0.00 | 0.18 | |
| individualCall | 0.16 | 0.03 | 0.19 | |
| iniCall-CNVDetectionResult-method | 0.17 | 0.00 | 0.17 | |
| iniCall | 0.17 | 0.00 | 0.18 | |
| integerCopyNumber-CNVDetectionResult-method | 0.17 | 0.00 | 0.17 | |
| integerCopyNumber | 0.16 | 0.00 | 0.15 | |
| localAssessments-CNVDetectionResult-method | 0.17 | 0.00 | 0.17 | |
| localAssessments | 0.23 | 0.02 | 0.25 | |
| makeRobustCNVR | 0.44 | 0.01 | 0.45 | |
| normalizeChromosomes | 0.21 | 0.00 | 0.20 | |
| normalizeGenome | 0.20 | 0.02 | 0.22 | |
| normalizedData-CNVDetectionResult-method | 0.25 | 0.03 | 0.28 | |
| normalizedData | 0.25 | 0.03 | 0.28 | |
| params-CNVDetectionResult-method | 0.22 | 0.00 | 0.24 | |
| params | 0.17 | 0.00 | 0.17 | |
| posteriorProbs-CNVDetectionResult-method | 0.20 | 0.02 | 0.22 | |
| posteriorProbs | 0.21 | 0.03 | 0.23 | |
| referencecn.mops | 14.15 | 0.00 | 23.13 | |
| sampleNames-CNVDetectionResult-method | 0.24 | 0.00 | 0.23 | |
| sampleNames | 0.25 | 0.00 | 0.25 | |
| segment | 0 | 0 | 0 | |
| segmentation-CNVDetectionResult-method | 0.16 | 0.00 | 0.16 | |
| segmentation | 0.16 | 0.00 | 0.16 | |
| segplot-CNVDetectionResult-method | 0.73 | 0.02 | 0.75 | |
| segplot | 0.75 | 0.00 | 0.75 | |
| singlecn.mops | 0.52 | 0.01 | 0.53 | |