H. Pagès
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SplicingGraphs |
| git_branch: RELEASE_3_13 |
| git_last_commit: 6066f74 |
| git_last_commit_date: 2021-05-19 11:58:48 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:24 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the SplicingGraphs package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SplicingGraphs.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1830/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SplicingGraphs 1.32.0 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: SplicingGraphs |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SplicingGraphs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SplicingGraphs_1.32.0.tar.gz |
| StartedAt: 2021-10-15 06:05:54 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:41:28 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 2134.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SplicingGraphs.Rcheck |
| Warnings: 3 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SplicingGraphs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SplicingGraphs_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SplicingGraphs.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.32.0'
* package encoding: UTF-8
* 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 'SplicingGraphs' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SplicingGraphs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'GenomicFeatures' 'GenomicAlignments' 'Rgraphviz' 'igraph'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'igraph' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
'S4Vectors:::selfmatchIntegerPairs'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
'IRanges:::regroupBySupergroup' 'IRanges:::unlist_as_integer'
'S4Vectors:::setPrototypeFromObject'
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 ... WARNING
Undocumented code objects:
'reportReads'
Undocumented S4 methods:
generic '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
generic 'reportReads' and siglist 'SplicingGraphs'
generic 'updateObject' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
'reportReads'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotTranscripts-methods 40.49 1.00 101.97
toy_data 21.37 0.00 21.37
countReads-methods 8.62 0.04 69.22
sgedges-methods 7.30 0.02 69.43
rsgedgesByGene-methods 5.98 0.25 66.38
sgedgesByGene-methods 5.56 0.03 69.05
txpath-methods 5.45 0.06 67.72
assignReads 5.30 0.02 64.79
bubbles-methods 4.94 0.06 67.86
SplicingGraphs-class 4.81 0.06 65.83
sgraph-methods 4.10 0.08 67.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotTranscripts-methods 50.22 0.27 119.47
toy_data 24.69 0.02 24.70
countReads-methods 10.31 0.08 83.84
sgedges-methods 9.00 0.03 76.01
rsgedgesByGene-methods 7.17 0.03 76.47
assignReads 6.64 0.02 74.16
sgedgesByGene-methods 6.55 0.06 74.52
txpath-methods 6.34 0.08 73.00
bubbles-methods 6.13 0.01 73.78
SplicingGraphs-class 5.31 0.09 73.92
sgraph-methods 4.65 0.11 71.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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: 3 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.
SplicingGraphs.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SplicingGraphs_1.32.0.tar.gz && rm -rf SplicingGraphs.buildbin-libdir && mkdir SplicingGraphs.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SplicingGraphs_1.32.0.zip && rm SplicingGraphs_1.32.0.tar.gz SplicingGraphs_1.32.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
7 45.5M 7 3308k 0 0 3248k 0 0:00:14 0:00:01 0:00:13 3247k
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29 45.5M 29 13.2M 0 0 4496k 0 0:00:10 0:00:03 0:00:07 4496k
39 45.5M 39 18.1M 0 0 4640k 0 0:00:10 0:00:04 0:00:06 4640k
54 45.5M 54 24.6M 0 0 5038k 0 0:00:09 0:00:05 0:00:04 5075k
71 45.5M 71 32.5M 0 0 5547k 0 0:00:08 0:00:06 0:00:02 6016k
90 45.5M 90 41.1M 0 0 5983k 0 0:00:07 0:00:07 --:--:-- 6733k
100 45.5M 100 45.5M 0 0 6098k 0 0:00:07 0:00:07 --:--:-- 7138k
install for i386
* installing *source* package 'SplicingGraphs' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** help
*** installing help indices
converting help for package 'SplicingGraphs'
finding HTML links ... done
SplicingGraphs-class html
SplicingGraphs-package html
TSPCsg html
assignReads html
bubbles-methods html
countReads-methods html
plotTranscripts-methods html
rsgedgesByGene-methods html
sgedges-methods html
sgedgesByGene-methods html
sgraph-methods html
toy_data html
txpath-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.32.0.zip
* DONE (SplicingGraphs)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SplicingGraphs' successfully unpacked and MD5 sums checked
|
SplicingGraphs.Rcheck/tests_i386/run_unitTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> require("SplicingGraphs") || stop("unable to load SplicingGraphs package")
Loading required package: SplicingGraphs
Loading required package: GenomicFeatures
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:Biostrings':
complement
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
> SplicingGraphs:::.test()
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
RUNIT TEST PROTOCOL -- Fri Oct 15 06:40:03 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
SplicingGraphs RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
16.54 1.37 64.93
|
SplicingGraphs.Rcheck/tests_x64/run_unitTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> require("SplicingGraphs") || stop("unable to load SplicingGraphs package")
Loading required package: SplicingGraphs
Loading required package: GenomicFeatures
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:Biostrings':
complement
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
> SplicingGraphs:::.test()
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
RUNIT TEST PROTOCOL -- Fri Oct 15 06:41:14 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
SplicingGraphs RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.12 0.62 70.37
|
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SplicingGraphs.Rcheck/examples_i386/SplicingGraphs-Ex.timings
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SplicingGraphs.Rcheck/examples_x64/SplicingGraphs-Ex.timings
|