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 13:42:40 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.6.0.tar.gz |
| StartedAt: 2018-04-12 05:26:20 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:32:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 370.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: isomiRs.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isomiRs_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘isomiRs’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘BiocGenerics::normalize’ by ‘TMB::normalize’ when loading ‘isomiRs’
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 19.7Mb
sub-directories of 1Mb or more:
data 7.1Mb
libs 12.1Mb
* 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoLQNO 15.183 0.154 15.666
isoCorrect 5.360 0.183 5.614
isoDE 5.214 0.172 5.494
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/00check.log’
for details.
isomiRs.Rcheck/00install.out
* installing *source* package ‘isomiRs’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c LQNO_DE.cpp -o LQNO_DE.o
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LQNO_DE.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/TMB/include/TMB.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
13 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o isomiRs.so LQNO_DE.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/isomiRs.Rcheck/isomiRs/libs
** 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
** 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’
* DONE (isomiRs)
isomiRs.Rcheck/tests/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-apple-darwin15.6.0 (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
22.941 0.933 24.264
isomiRs.Rcheck/isomiRs-Ex.timings
| name | user | system | elapsed | |
| IsomirDataSeq | 1.133 | 0.011 | 1.154 | |
| IsomirDataSeqFromFiles | 0.600 | 0.002 | 0.608 | |
| counts | 2.477 | 0.154 | 2.672 | |
| design | 1.173 | 0.063 | 1.267 | |
| findTargets | 0.147 | 0.001 | 0.151 | |
| isoCorrect | 5.360 | 0.183 | 5.614 | |
| isoCounts | 2.113 | 0.155 | 2.280 | |
| isoDE | 5.214 | 0.172 | 5.494 | |
| isoLQNO | 15.183 | 0.154 | 15.666 | |
| isoNetwork | 0.832 | 0.024 | 0.883 | |
| isoNorm | 3.691 | 0.150 | 3.924 | |
| isoPLSDA | 3.448 | 0.189 | 3.704 | |
| isoPLSDAplot | 3.079 | 0.229 | 3.372 | |
| isoPlot | 2.666 | 0.097 | 2.792 | |
| isoPlotPosition | 1.822 | 0.072 | 1.924 | |
| isoSelect | 1.416 | 0.104 | 1.537 | |
| isoTop | 1.320 | 0.051 | 1.383 | |