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 11:40:27 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: cn.mops |
| Version: 1.49.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings cn.mops_1.49.0.tar.gz |
| StartedAt: 2024-03-28 03:58:19 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:02:46 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 267.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings cn.mops_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘1.49.0’
* 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 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 30.342 0.126 41.080
calcFractionalCopyNumbers-CNVDetectionResult-method 17.925 0.020 17.962
calcFractionalCopyNumbers 17.695 0.004 17.714
cn.mops 8.139 0.189 21.990
haplocn.mops 1.400 0.024 12.567
getReadCountsFromBAM 0.569 0.002 6.090
getSegmentReadCountsFromBAM 0.369 0.004 5.848
* 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.
cn.mops.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL cn.mops
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0.002 | 0.000 | 0.001 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 17.925 | 0.020 | 17.962 | |
| calcFractionalCopyNumbers | 17.695 | 0.004 | 17.714 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.520 | 0.000 | 0.521 | |
| calcIntegerCopyNumbers | 0.490 | 0.004 | 0.495 | |
| cn.mops | 8.139 | 0.189 | 21.990 | |
| cnvr-CNVDetectionResult-method | 0.301 | 0.008 | 0.312 | |
| cnvr | 0.280 | 0.004 | 0.286 | |
| cnvs-CNVDetectionResult-method | 0.279 | 0.000 | 0.282 | |
| cnvs | 0.265 | 0.004 | 0.270 | |
| exomecn.mops | 3.458 | 0.004 | 3.469 | |
| getReadCountsFromBAM | 0.569 | 0.002 | 6.090 | |
| getSegmentReadCountsFromBAM | 0.369 | 0.004 | 5.848 | |
| gr-CNVDetectionResult-method | 0.289 | 0.000 | 0.291 | |
| gr | 0.284 | 0.000 | 0.285 | |
| haplocn.mops | 1.400 | 0.024 | 12.567 | |
| individualCall-CNVDetectionResult-method | 0.279 | 0.004 | 0.283 | |
| individualCall | 0.304 | 0.000 | 0.304 | |
| iniCall-CNVDetectionResult-method | 0.296 | 0.000 | 0.297 | |
| iniCall | 0.280 | 0.000 | 0.281 | |
| integerCopyNumber-CNVDetectionResult-method | 0.297 | 0.000 | 0.299 | |
| integerCopyNumber | 0.275 | 0.008 | 0.283 | |
| localAssessments-CNVDetectionResult-method | 0.278 | 0.000 | 0.278 | |
| localAssessments | 0.287 | 0.000 | 0.288 | |
| makeRobustCNVR | 0.485 | 0.000 | 0.486 | |
| normalizeChromosomes | 0.234 | 0.000 | 0.234 | |
| normalizeGenome | 0.245 | 0.004 | 0.250 | |
| normalizedData-CNVDetectionResult-method | 0.289 | 0.004 | 0.294 | |
| normalizedData | 0.286 | 0.004 | 0.291 | |
| params-CNVDetectionResult-method | 0.264 | 0.004 | 0.269 | |
| params | 0.293 | 0.000 | 0.293 | |
| posteriorProbs-CNVDetectionResult-method | 0.270 | 0.003 | 0.275 | |
| posteriorProbs | 0.260 | 0.008 | 0.269 | |
| referencecn.mops | 30.342 | 0.126 | 41.080 | |
| sampleNames-CNVDetectionResult-method | 0.278 | 0.004 | 0.284 | |
| sampleNames | 0.275 | 0.000 | 0.275 | |
| segment | 0.024 | 0.004 | 0.028 | |
| segmentation-CNVDetectionResult-method | 0.299 | 0.000 | 0.300 | |
| segmentation | 0.278 | 0.004 | 0.283 | |
| segplot-CNVDetectionResult-method | 1.260 | 0.004 | 1.266 | |
| segplot | 1.268 | 0.008 | 1.279 | |
| singlecn.mops | 0.954 | 0.000 | 0.955 | |