Aaron Lun
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/InteractionSet |
| Branch: RELEASE_3_6 |
| Last Commit: 22b7b2c |
| Last Changed Date: 2017-10-30 12:41:16 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:28:01 -0400 (Thu, 12 Apr 2018).
| Package 700/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InteractionSet 1.6.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: InteractionSet |
| Version: 1.6.0 |
| Command: rm -rf InteractionSet.buildbin-libdir InteractionSet.Rcheck && mkdir InteractionSet.buildbin-libdir InteractionSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InteractionSet.buildbin-libdir InteractionSet_1.6.0.tar.gz >InteractionSet.Rcheck\00install.out 2>&1 && cp InteractionSet.Rcheck\00install.out InteractionSet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InteractionSet.buildbin-libdir --install="check:InteractionSet-install.out" --force-multiarch --no-vignettes --timings InteractionSet_1.6.0.tar.gz |
| StartedAt: 2018-04-12 00:50:54 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:56:52 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 358.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InteractionSet.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf InteractionSet.buildbin-libdir InteractionSet.Rcheck && mkdir InteractionSet.buildbin-libdir InteractionSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InteractionSet.buildbin-libdir InteractionSet_1.6.0.tar.gz >InteractionSet.Rcheck\00install.out 2>&1 && cp InteractionSet.Rcheck\00install.out InteractionSet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InteractionSet.buildbin-libdir --install="check:InteractionSet-install.out" --force-multiarch --no-vignettes --timings InteractionSet_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InteractionSet.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 'InteractionSet/DESCRIPTION' ... OK * this is package 'InteractionSet' 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 ... OK * checking for portable file names ... OK * checking whether package 'InteractionSet' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-class.Rd:42: missing file link 'Annotated' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-class.Rd:51: missing file link 'Annotated' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:33: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:37: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:100: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/interaction-accessors.Rd:170: missing file link 'mcols' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/interaction-compare.Rd:216: missing file link 'pcompare' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:138: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:142: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:171: missing file link 'findOverlaps' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:284: missing file link 'findOverlaps' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InteractionSet.Rcheck/00install.out' for details. * 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 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 * 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'GenomicRanges:::extraColumnSlotNames' 'S4Vectors:::disableValidity' 'S4Vectors:::makeClassinfoRowForCompactPrinting' 'S4Vectors:::makePrettyMatrixForCompactPrinting' 'S4Vectors:::selectSome' 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 ... 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 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/InteractionSet.buildbin-libdir/InteractionSet/libs/i386/InteractionSet.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 ** running examples for arch 'x64' ... OK * 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InteractionSet.Rcheck/00check.log' for details.
InteractionSet.Rcheck/00install.out
install for i386
* installing *source* package 'InteractionSet' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c box_bounds.cpp -o box_bounds.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c overlaps.cpp -o overlaps.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o InteractionSet.dll tmp.def box_bounds.o init.o overlaps.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/InteractionSet.buildbin-libdir/InteractionSet/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'InteractionSet'
finding HTML links ... done
ContactMatrix-accessors html
finding level-2 HTML links ... done
ContactMatrix-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-class.Rd:42: missing file link 'Annotated'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-class.Rd:51: missing file link 'Annotated'
ContactMatrix-distances html
ContactMatrix-overlaps html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:33: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:37: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/ContactMatrix-overlaps.Rd:100: missing file link 'findOverlaps'
ContactMatrix-sorting html
ContactMatrix-subset html
GInteractions-class html
InteractionSet-class html
boundingBox html
conversion html
distances html
granges-methods html
interaction-accessors html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/interaction-accessors.Rd:170: missing file link 'mcols'
interaction-bind html
interaction-compare html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/interaction-compare.Rd:216: missing file link 'pcompare'
interaction-subset html
linearize html
linkOverlaps html
overlaps html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:138: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:142: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:171: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaY6r9/R.INSTALL2c5847e04167/InteractionSet/man/overlaps.Rd:284: missing file link 'findOverlaps'
pairs html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'InteractionSet' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c box_bounds.cpp -o box_bounds.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c overlaps.cpp -o overlaps.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o InteractionSet.dll tmp.def box_bounds.o init.o overlaps.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/InteractionSet.buildbin-libdir/InteractionSet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InteractionSet' as InteractionSet_1.6.0.zip
* DONE (InteractionSet)
In R CMD INSTALL
In R CMD INSTALL
|
InteractionSet.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(InteractionSet)
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: SummarizedExperiment
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
>
> test_check("InteractionSet")
== testthat results ===========================================================
OK: 1663 SKIPPED: 0 FAILED: 0
>
>
> proc.time()
user system elapsed
52.31 0.39 52.70
|
InteractionSet.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(InteractionSet)
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: SummarizedExperiment
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
>
> test_check("InteractionSet")
== testthat results ===========================================================
OK: 1663 SKIPPED: 0 FAILED: 0
>
>
> proc.time()
user system elapsed
66.45 0.20 67.87
|
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InteractionSet.Rcheck/examples_i386/InteractionSet-Ex.timings
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InteractionSet.Rcheck/examples_x64/InteractionSet-Ex.timings
|