Henry Miller
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/RLSeq |
| git_branch: RELEASE_3_14 |
| git_last_commit: 191326e |
| git_last_commit_date: 2021-10-26 13:14:18 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:14 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the RLSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RLSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1619/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RLSeq 1.0.0 (landing page) Henry Miller
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RLSeq |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RLSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RLSeq_1.0.0.tar.gz |
| StartedAt: 2022-04-13 01:47:17 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:07:39 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1221.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RLSeq.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RLSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RLSeq_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RLSeq.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RLSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RLSeq' version '1.0.0'
* 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 'RLSeq' can be installed ... OK
* 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 ... OK
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RLSeq 39.92 2.69 43.84
predictCondition 22.79 1.66 25.71
geneAnnotation 17.83 0.65 25.94
plotEnrichment 16.53 0.71 18.31
featureEnrich 16.89 0.32 18.57
plotRLRegionOverlap 15.05 0.83 17.79
analyzeRLFS 12.61 0.08 13.05
corrHeatmap 8.69 1.55 10.68
RLRangesFromRLBase 7.73 2.27 11.91
rlRegionTest 7.08 0.14 7.64
report 0.68 0.08 68.57
** running examples for arch 'x64' ... ERROR
Running examples in 'RLSeq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report
> ### Title: RLSeq Report
> ### Aliases: report
>
> ### ** Examples
>
>
> # Example data with RLSeq() already run.
> rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))
>
> # Get a TMP file (only for example usae)
> tmp <- tempfile()
>
> # Generate the report
> report(rlr, reportPath = tmp)
Error in data$sofile[[paste0("arch-", .Platform$r_arch)]] :
subscript out of bounds
Calls: <Anonymous>
Execution halted
Error: <callr_status_error in get_result(output = out, options):
callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed>
Stack trace:
1. RLSeq:::report(rlr, reportPath = tmp)
2. callr::r(function(template, object, reportPath, quiet, ...) { ...
3. callr:::get_result(output = out, options)
4. throw(new_callr_error(output, killmsg))
x callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Execution halted
* 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 ERROR
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/RLSeq.Rcheck/00check.log'
for details.
RLSeq.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RLSeq_1.0.0.tar.gz && rm -rf RLSeq.buildbin-libdir && mkdir RLSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RLSeq.buildbin-libdir RLSeq_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RLSeq_1.0.0.zip && rm RLSeq_1.0.0.tar.gz RLSeq_1.0.0.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
1 1610k 1 30837 0 0 253k 0 0:00:06 --:--:-- 0:00:06 253k
62 1610k 62 1009k 0 0 916k 0 0:00:01 0:00:01 --:--:-- 916k
100 1610k 100 1610k 0 0 1094k 0 0:00:01 0:00:01 --:--:-- 1094k
install for i386
* installing *source* package 'RLSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RLSeq'
finding HTML links ... done
RLRanges html
RLRangesFromRLBase html
RLResults html
RLSeq html
analyzeRLFS html
auxdata html
available_genomes html
checkRLFSAnno html
corrAnalyze html
corrHeatmap html
featureEnrich html
feature_ggplot html
geneAnnotation html
genomeMasks html
getChromSizes html
getGSSignal html
getRLFSAnno html
peak_stats html
plotEnrichment html
plotRLFSRes html
plotRLRegionOverlap html
predictCondition html
report html
rlRegionTest html
tableToRegions html
urlExists html
** 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
install for x64
* installing *source* package 'RLSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RLSeq' as RLSeq_1.0.0.zip
* DONE (RLSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RLSeq' successfully unpacked and MD5 sums checked
|
RLSeq.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(RLSeq)
>
> test_check("RLSeq")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
snapshotDate(): 2021-10-19
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
snapshotDate(): 2021-10-20
Loading required package: GenomicFeatures
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")'.
228 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
snapshotDate(): 2021-10-20
228 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
193.06 12.21 216.11
|
RLSeq.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(RLSeq)
>
> test_check("RLSeq")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
snapshotDate(): 2021-10-19
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
snapshotDate(): 2021-10-20
Loading required package: GenomicFeatures
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")'.
228 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 10 permutations is 0.0909090909090909. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
snapshotDate(): 2021-10-20
228 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
179.78 6.76 196.64
|
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RLSeq.Rcheck/examples_i386/RLSeq-Ex.timings
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RLSeq.Rcheck/examples_x64/RLSeq-Ex.timings
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