Lorena Pantano
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/isomiRs |
| Branch: RELEASE_3_6 |
| Last Commit: 8e254fe |
| Last Changed Date: 2017-10-30 12:41:15 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:50 -0400 (Thu, 12 Apr 2018).
| Package 719/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| isomiRs 1.6.0 Lorena Pantano
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: isomiRs |
| Version: 1.6.0 |
| Command: rm -rf isomiRs.buildbin-libdir isomiRs.Rcheck && mkdir isomiRs.buildbin-libdir isomiRs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isomiRs.buildbin-libdir isomiRs_1.6.0.tar.gz >isomiRs.Rcheck\00install.out 2>&1 && cp isomiRs.Rcheck\00install.out isomiRs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=isomiRs.buildbin-libdir --install="check:isomiRs-install.out" --force-multiarch --no-vignettes --timings isomiRs_1.6.0.tar.gz |
| StartedAt: 2018-04-12 00:55:34 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:04:30 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 536.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: isomiRs.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### rm -rf isomiRs.buildbin-libdir isomiRs.Rcheck && mkdir isomiRs.buildbin-libdir isomiRs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isomiRs.buildbin-libdir isomiRs_1.6.0.tar.gz >isomiRs.Rcheck\00install.out 2>&1 && cp isomiRs.Rcheck\00install.out isomiRs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=isomiRs.buildbin-libdir --install="check:isomiRs-install.out" --force-multiarch --no-vignettes --timings isomiRs_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isomiRs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'isomiRs' version '1.6.0'
* 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 ... 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 whether package 'isomiRs' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/IsomirDataSeq.Rd:10: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/IsomirDataSeqFromFiles.Rd:35: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/findTargets.Rd:11: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/findTargets.Rd:14: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:11: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:14: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:20: missing file link 'AnnotationDb'
Warning: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 26.8Mb
sub-directories of 1Mb or more:
data 7.1Mb
libs 19.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
.run_enricher: no visible binding for global variable 'sel_genes'
.run_enricher: no visible global function definition for 'enrichGO'
.run_enricher: no visible binding for global variable 'Count'
.viz_mirna_gene_enrichment: no visible binding for global variable 'X1'
isoNetwork : <anonymous>: no visible binding for global variable 'X1'
isoNetwork : <anonymous>: no visible binding for global variable 'X2'
isoNetwork: no visible binding for global variable 'go'
isoPlotNet: no visible binding for global variable 'ngene'
Undefined global functions or variables:
Count X1 X2 enrichGO go ngene sel_genes
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.buildbin-libdir/isomiRs/libs/i386/isomiRs.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoLQNO 17.73 1.08 19.92
isoDE 5.05 0.11 5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoLQNO 17.06 0.21 17.42
isoDE 5.45 0.08 5.53
isoCorrect 5.00 0.06 5.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/00check.log'
for details.
isomiRs.Rcheck/00install.out
install for i386
* installing *source* package 'isomiRs' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/TMB/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c LQNO_DE.cpp -o LQNO_DE.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o isomiRs.dll tmp.def LQNO_DE.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.buildbin-libdir/isomiRs/libs/i386
** R
** data
*** moving datasets to lazyload DB
Warning in checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.2.12
Current Matrix version is 1.2.14
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
Warning: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
** help
*** installing help indices
converting help for package 'isomiRs'
finding HTML links ... done
IsomirDataSeq html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/IsomirDataSeq.Rd:10: missing file link 'SummarizedExperiment'
IsomirDataSeqFromFiles html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/IsomirDataSeqFromFiles.Rd:35: missing file link 'SummarizedExperiment'
LQNO html
counts html
dat286.long html
design html
findTargets html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/findTargets.Rd:11: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/findTargets.Rd:14: missing file link 'SummarizedExperiment'
gene_ex_rse html
isoCorrect html
isoCounts html
isoDE html
isoLQNO html
isoNetwork html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:11: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:14: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp06FE1a/R.INSTALL235c79d4cfe/isomiRs/man/isoNetwork.Rd:20: missing file link 'AnnotationDb'
isoNorm html
isoPLSDA html
isoPLSDAplot html
isoPlot html
isoPlotNet html
isoPlotPosition html
isoSelect html
isoTop html
isomiRs-package html
ma_ex html
mirData html
mirTritation html
mirna_ex_rse html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.2.12
Current Matrix version is 1.2.14
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
Warning: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
In R CMD INSTALL
install for x64
* installing *source* package 'isomiRs' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/TMB/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c LQNO_DE.cpp -o LQNO_DE.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o isomiRs.dll tmp.def LQNO_DE.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.buildbin-libdir/isomiRs/libs/x64
** testing if installed package can be loaded
Warning in checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.2.12
Current Matrix version is 1.2.14
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
Warning: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
* MD5 sums
packaged installation of 'isomiRs' as isomiRs_1.6.0.zip
* DONE (isomiRs)
In R CMD INSTALL
In R CMD INSTALL
|
isomiRs.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(isomiRs)
Loading required package: DiscriMiner
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: TMB
Attaching package: 'TMB'
The following object is masked from 'package:BiocGenerics':
normalize
Loading required package: RcppEigen
Warning messages:
1: In checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.2.12
Current Matrix version is 1.2.14
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
2: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
>
> test_check("isomiRs")
Dimmension of cor matrix: 20 25
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 0 0
== testthat results ===========================================================
OK: 30 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.89 0.84 21.73
|
isomiRs.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(isomiRs)
Loading required package: DiscriMiner
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: TMB
Attaching package: 'TMB'
The following object is masked from 'package:BiocGenerics':
normalize
Loading required package: RcppEigen
Warning messages:
1: In checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.2.12
Current Matrix version is 1.2.14
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
2: replacing previous import 'BiocGenerics::normalize' by 'TMB::normalize' when loading 'isomiRs'
>
> test_check("isomiRs")
Dimmension of cor matrix: 20 25
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 0 0
== testthat results ===========================================================
OK: 30 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
22.93 0.42 23.34
|
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isomiRs.Rcheck/examples_i386/isomiRs-Ex.timings
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isomiRs.Rcheck/examples_x64/isomiRs-Ex.timings
|