Benjamin Haibe-Kains
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/genefu |
| Branch: RELEASE_3_10 |
| Last Commit: 41b962e |
| Last Changed Date: 2020-01-31 16:18:01 -0400 (Fri, 31 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:06:19 -0400 (Wed, 15 Apr 2020).
| Package 653/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genefu 2.18.1 Benjamin Haibe-Kains
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: genefu |
| Version: 2.18.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings genefu_2.18.1.tar.gz |
| StartedAt: 2020-04-15 00:59:04 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:01:42 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 157.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genefu.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings genefu_2.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/genefu.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.18.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'survcomp', 'mclust', 'limma', 'biomaRt', 'iC10', 'AIMS'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 5.1Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘mclust:::grid1’ ‘mclust:::grid2’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
claudinLow: no visible global function definition for ‘standardize’
Undefined global functions or variables:
standardize
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘multilevel’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/genefu.Rcheck/00check.log’
for details.
genefu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL genefu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘genefu’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (genefu)
genefu.Rcheck/genefu-Ex.timings
| name | user | system | elapsed | |
| bimod | 0.236 | 0.012 | 0.249 | |
| boxplotplus2 | 0.008 | 0.000 | 0.008 | |
| claudinLow | 1.052 | 0.000 | 1.050 | |
| claudinLowData | 0.032 | 0.000 | 0.031 | |
| compare.proto.cor | 1.072 | 0.012 | 1.085 | |
| compute.pairw.cor.meta | 1.284 | 0.000 | 1.283 | |
| compute.proto.cor.meta | 0.948 | 0.008 | 0.958 | |
| cordiff.dep | 0.012 | 0.000 | 0.011 | |
| endoPredict | 0.016 | 0.000 | 0.015 | |
| expos | 0.000 | 0.000 | 0.002 | |
| fuzzy.ttest | 0.004 | 0.000 | 0.000 | |
| gene70 | 0.136 | 0.004 | 0.142 | |
| gene76 | 0.044 | 0.000 | 0.041 | |
| geneid.map | 0.084 | 0.000 | 0.086 | |
| genius | 0.196 | 0.008 | 0.203 | |
| ggi | 0.080 | 0.000 | 0.078 | |
| ihc4 | 0.004 | 0.000 | 0.006 | |
| intrinsic.cluster | 0.228 | 0.000 | 0.213 | |
| intrinsic.cluster.predict | 0.132 | 0.000 | 0.133 | |
| map.datasets | 0.796 | 0.004 | 0.799 | |
| mod1 | 0.004 | 0.000 | 0.001 | |
| mod2 | 0.000 | 0.000 | 0.001 | |
| modelOvcAngiogenic | 0.000 | 0.000 | 0.001 | |
| molecular.subtyping | 3.372 | 0.032 | 3.530 | |
| nkis | 0.000 | 0.000 | 0.002 | |
| npi | 0.004 | 0.004 | 0.007 | |
| oncotypedx | 0.064 | 0.000 | 0.061 | |
| ovcAngiogenic | 0.112 | 0.004 | 0.115 | |
| ovcCrijns | 0.108 | 0.004 | 0.114 | |
| ovcTCGA | 0.28 | 0.00 | 0.28 | |
| ovcYoshihara | 0.076 | 0.000 | 0.078 | |
| pam50 | 0.020 | 0.000 | 0.018 | |
| pik3cags | 0.048 | 0.000 | 0.050 | |
| power.cor | 0.004 | 0.000 | 0.000 | |
| ps.cluster | 0.324 | 0.008 | 0.326 | |
| read.m.file | 0.032 | 0.000 | 0.050 | |
| rename.duplicate | 0.004 | 0.000 | 0.002 | |
| rescale | 0.056 | 0.000 | 0.056 | |
| rorS | 0.200 | 0.000 | 0.201 | |
| scmgene.robust | 0.008 | 0.000 | 0.007 | |
| scmod1.robust | 0.008 | 0.000 | 0.008 | |
| scmod2.robust | 0.008 | 0.000 | 0.008 | |
| setcolclass.df | 0.000 | 0.004 | 0.003 | |
| sig.endoPredict | 0.004 | 0.000 | 0.004 | |
| sig.gene70 | 0.008 | 0.000 | 0.006 | |
| sig.gene76 | 0.000 | 0.004 | 0.007 | |
| sig.genius | 0.028 | 0.000 | 0.030 | |
| sig.ggi | 0.008 | 0.000 | 0.006 | |
| sig.oncotypedx | 0.000 | 0.004 | 0.005 | |
| sig.pik3cags | 0.004 | 0.000 | 0.003 | |
| sig.score | 0.092 | 0.004 | 0.096 | |
| sig.tamr13 | 0.000 | 0.004 | 0.006 | |
| sigOvcAngiogenic | 0.004 | 0.000 | 0.008 | |
| sigOvcCrijns | 0.004 | 0.000 | 0.006 | |
| sigOvcSpentzos | 0.000 | 0.004 | 0.007 | |
| sigOvcTCGA | 0.008 | 0.000 | 0.009 | |
| sigOvcYoshihara | 0.004 | 0.004 | 0.007 | |
| spearmanCI | 0.000 | 0.000 | 0.001 | |
| ssp2003 | 0.04 | 0.00 | 0.04 | |
| ssp2006 | 0.052 | 0.000 | 0.054 | |
| st.gallen | 0.004 | 0.004 | 0.019 | |
| stab.fs | 0.136 | 0.000 | 0.137 | |
| stab.fs.ranking | 0.984 | 0.020 | 1.003 | |
| strescR | 0.000 | 0.000 | 0.002 | |
| subtype.cluster | 0.576 | 0.020 | 0.599 | |
| subtype.cluster.predict | 0.172 | 0.000 | 0.172 | |
| tamr13 | 0.048 | 0.000 | 0.045 | |
| tbrm | 0.000 | 0.000 | 0.001 | |
| vdxs | 0.004 | 0.000 | 0.001 | |
| weighted.meanvar | 0.000 | 0.000 | 0.001 | |
| write.m.file | 0.004 | 0.000 | 0.001 | |