Gundula Povysil
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:53 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 385/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.mops 1.50.0 (landing page) Gundula Povysil
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.50.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cn.mops_1.50.0.tar.gz |
| StartedAt: 2024-05-31 02:23:39 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 02:26:54 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 195.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 7.676 0.053 16.354
cn.mops 5.379 0.111 15.570
calcFractionalCopyNumbers-CNVDetectionResult-method 5.276 0.016 5.292
calcFractionalCopyNumbers 5.087 0.007 5.095
haplocn.mops 0.985 0.012 10.186
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL cn.mops
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cnmops.cpp -o cnmops.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/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:59:27: 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:
/home/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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/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 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 5.276 | 0.016 | 5.292 | |
| calcFractionalCopyNumbers | 5.087 | 0.007 | 5.095 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.38 | 0.00 | 0.38 | |
| calcIntegerCopyNumbers | 0.337 | 0.000 | 0.338 | |
| cn.mops | 5.379 | 0.111 | 15.570 | |
| cnvr-CNVDetectionResult-method | 0.194 | 0.000 | 0.193 | |
| cnvr | 0.207 | 0.008 | 0.215 | |
| cnvs-CNVDetectionResult-method | 0.208 | 0.000 | 0.208 | |
| cnvs | 0.188 | 0.003 | 0.191 | |
| exomecn.mops | 2.176 | 0.028 | 2.204 | |
| getReadCountsFromBAM | 0.393 | 0.008 | 4.922 | |
| getSegmentReadCountsFromBAM | 0.261 | 0.012 | 4.813 | |
| gr-CNVDetectionResult-method | 0.201 | 0.016 | 0.217 | |
| gr | 0.201 | 0.004 | 0.205 | |
| haplocn.mops | 0.985 | 0.012 | 10.186 | |
| individualCall-CNVDetectionResult-method | 0.225 | 0.008 | 0.234 | |
| individualCall | 0.199 | 0.008 | 0.207 | |
| iniCall-CNVDetectionResult-method | 0.211 | 0.004 | 0.215 | |
| iniCall | 0.214 | 0.000 | 0.214 | |
| integerCopyNumber-CNVDetectionResult-method | 0.200 | 0.004 | 0.203 | |
| integerCopyNumber | 0.215 | 0.003 | 0.218 | |
| localAssessments-CNVDetectionResult-method | 0.215 | 0.000 | 0.215 | |
| localAssessments | 0.205 | 0.008 | 0.213 | |
| makeRobustCNVR | 0.348 | 0.000 | 0.348 | |
| normalizeChromosomes | 0.143 | 0.012 | 0.155 | |
| normalizeGenome | 0.156 | 0.000 | 0.157 | |
| normalizedData-CNVDetectionResult-method | 0.204 | 0.004 | 0.209 | |
| normalizedData | 0.216 | 0.000 | 0.216 | |
| params-CNVDetectionResult-method | 0.198 | 0.012 | 0.210 | |
| params | 0.209 | 0.008 | 0.216 | |
| posteriorProbs-CNVDetectionResult-method | 0.195 | 0.000 | 0.194 | |
| posteriorProbs | 0.195 | 0.000 | 0.195 | |
| referencecn.mops | 7.676 | 0.053 | 16.354 | |
| sampleNames-CNVDetectionResult-method | 0.190 | 0.000 | 0.191 | |
| sampleNames | 0.202 | 0.000 | 0.201 | |
| segment | 0.014 | 0.003 | 0.017 | |
| segmentation-CNVDetectionResult-method | 0.199 | 0.004 | 0.203 | |
| segmentation | 0.199 | 0.005 | 0.204 | |
| segplot-CNVDetectionResult-method | 0.818 | 0.004 | 0.822 | |
| segplot | 0.808 | 0.019 | 0.828 | |
| singlecn.mops | 0.605 | 0.004 | 0.609 | |