Gundula Povysil
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 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 -0400 (Fri, 19 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:30 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 382/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.mops 1.49.0 (landing page) Gundula Povysil
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: cn.mops |
| Version: 1.49.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cn.mops_1.49.0.tar.gz |
| StartedAt: 2024-03-28 00:36:32 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 00:40:29 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 236.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cn.mops.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cn.mops_1.49.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.49.0'
* 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 whether package 'cn.mops' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/cn.mops/libs/x64/cn.mops.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 nor [v]sprintf. 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 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 15.20 0.12 26.61
calcFractionalCopyNumbers 10.29 0.10 10.38
calcFractionalCopyNumbers-CNVDetectionResult-method 10.22 0.06 10.36
cn.mops 8.05 0.21 21.69
haplocn.mops 1.25 0.02 12.04
getReadCountsFromBAM 0.46 0.06 6.40
getSegmentReadCountsFromBAM 0.29 0.02 5.46
* 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
'F:/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck/00check.log'
for details.
cn.mops.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL cn.mops
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'cn.mops' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cnmops.cpp -o cnmops.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:
F:/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 -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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
** 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)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0 | 0 | 0 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.22 | 0.06 | 10.36 | |
| calcFractionalCopyNumbers | 10.29 | 0.10 | 10.38 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.42 | 0.00 | 0.42 | |
| calcIntegerCopyNumbers | 0.45 | 0.01 | 0.47 | |
| cn.mops | 8.05 | 0.21 | 21.69 | |
| cnvr-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 | |
| cnvr | 0.25 | 0.03 | 0.28 | |
| cnvs-CNVDetectionResult-method | 0.33 | 0.00 | 0.33 | |
| cnvs | 0.23 | 0.01 | 0.26 | |
| exomecn.mops | 3.42 | 0.02 | 3.44 | |
| getReadCountsFromBAM | 0.46 | 0.06 | 6.40 | |
| getSegmentReadCountsFromBAM | 0.29 | 0.02 | 5.46 | |
| gr-CNVDetectionResult-method | 0.25 | 0.01 | 0.26 | |
| gr | 0.31 | 0.00 | 0.32 | |
| haplocn.mops | 1.25 | 0.02 | 12.04 | |
| individualCall-CNVDetectionResult-method | 0.29 | 0.03 | 0.32 | |
| individualCall | 0.31 | 0.03 | 0.34 | |
| iniCall-CNVDetectionResult-method | 0.33 | 0.02 | 0.34 | |
| iniCall | 0.31 | 0.01 | 0.33 | |
| integerCopyNumber-CNVDetectionResult-method | 0.67 | 0.03 | 0.70 | |
| integerCopyNumber | 0.22 | 0.05 | 0.27 | |
| localAssessments-CNVDetectionResult-method | 0.30 | 0.03 | 0.33 | |
| localAssessments | 0.23 | 0.02 | 0.25 | |
| makeRobustCNVR | 0.36 | 0.03 | 0.39 | |
| normalizeChromosomes | 0.11 | 0.05 | 0.15 | |
| normalizeGenome | 0.14 | 0.06 | 0.21 | |
| normalizedData-CNVDetectionResult-method | 0.30 | 0.00 | 0.29 | |
| normalizedData | 0.26 | 0.01 | 0.29 | |
| params-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 | |
| params | 0.26 | 0.02 | 0.28 | |
| posteriorProbs-CNVDetectionResult-method | 0.24 | 0.00 | 0.24 | |
| posteriorProbs | 0.25 | 0.02 | 0.26 | |
| referencecn.mops | 15.20 | 0.12 | 26.61 | |
| sampleNames-CNVDetectionResult-method | 0.28 | 0.02 | 0.30 | |
| sampleNames | 0.25 | 0.01 | 0.28 | |
| segment | 0.02 | 0.00 | 0.02 | |
| segmentation-CNVDetectionResult-method | 0.22 | 0.02 | 0.23 | |
| segmentation | 0.23 | 0.01 | 0.25 | |
| segplot-CNVDetectionResult-method | 1.08 | 0.03 | 1.11 | |
| segplot | 1.06 | 0.02 | 1.08 | |
| singlecn.mops | 0.60 | 0.02 | 0.61 | |