Ulrich Bodenhofer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/podkat |
| Branch: RELEASE_3_11 |
| Last Commit: c8637db |
| Last Changed Date: 2020-04-27 14:47:48 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:24 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE podkat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1330/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| podkat 1.20.0 Ulrich Bodenhofer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: podkat |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:podkat.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings podkat_1.20.0.tar.gz |
| StartedAt: 2020-10-17 04:11:40 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:17:25 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 344.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: podkat.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:podkat.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings podkat_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/podkat.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘podkat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘podkat’ version ‘1.20.0’
* 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 ‘podkat’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 6.3Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/podkat/libs/podkat.so’:
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘srand48’, possibly from ‘srand48’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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
unmaskedRegions 31.794 3.622 40.918
assocTest-methods 13.537 0.352 13.890
plot-methods 11.678 0.700 12.379
GenotypeMatrix-class 5.507 0.051 8.253
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/podkat.Rcheck/00check.log’
for details.
podkat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL podkat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘podkat’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_podkat.cpp -o R_init_podkat.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bernoulliExact.cpp -o bernoulliExact.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c cumMax.cpp -o cumMax.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c doubleMale.cpp -o doubleMale.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c kernels.cpp -o kernels.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pValues.cpp -o pValues.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c partitionRegions.cpp -o partitionRegions.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c qfc.cpp -o qfc.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c readVariantInfo.cpp -o readVariantInfo.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-podkat/00new/podkat/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘p.adjust’ from package ‘stats’ in package ‘podkat’ Creating a generic function for ‘qqplot’ from package ‘stats’ in package ‘podkat’ ** 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 (podkat)
podkat.Rcheck/podkat-Ex.timings
| name | user | system | elapsed | |
| AssocTestResult-class | 0.910 | 0.032 | 0.961 | |
| AssocTestResultRanges-class | 1.966 | 0.148 | 2.113 | |
| GenotypeMatrix-class | 5.507 | 0.051 | 8.253 | |
| NullModel-class | 2.192 | 0.013 | 2.211 | |
| VariantInfo-class | 0.388 | 0.002 | 0.390 | |
| assocTest-methods | 13.537 | 0.352 | 13.890 | |
| computeKernel | 0.006 | 0.000 | 0.006 | |
| filterResult-methods | 1.679 | 0.000 | 1.680 | |
| genotypeMatrix-methods | 0.780 | 0.004 | 0.784 | |
| hgA | 0.026 | 0.000 | 0.026 | |
| nullModel-methods | 0.659 | 0.032 | 0.691 | |
| p.adjust-methods | 1.389 | 0.000 | 1.389 | |
| partitionRegions-methods | 0.931 | 0.000 | 0.931 | |
| plot-methods | 11.678 | 0.700 | 12.379 | |
| podkat-package | 1.288 | 0.004 | 1.292 | |
| print-methods | 1.988 | 0.008 | 1.996 | |
| qqplot-methods | 2.574 | 0.004 | 2.578 | |
| readGenotypeMatrix-methods | 0.254 | 0.000 | 0.253 | |
| readRegionsFromBedFile | 0.036 | 0.000 | 0.039 | |
| readSampleNamesFromVcfHeader | 0.035 | 0.000 | 0.035 | |
| readVariantInfo-methods | 0.305 | 0.000 | 0.305 | |
| sort-methods | 1.249 | 0.000 | 1.249 | |
| split-methods | 4.304 | 0.044 | 4.348 | |
| unmasked-datasets | 0.922 | 0.004 | 0.926 | |
| unmaskedRegions | 31.794 | 3.622 | 40.918 | |
| weightFuncs | 0.006 | 0.000 | 0.006 | |
| weights-methods | 1.477 | 0.008 | 1.485 | |