David Zhang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/megadepth |
| git_branch: RELEASE_3_14 |
| git_last_commit: 0e998eb |
| git_last_commit_date: 2021-10-26 13:04:18 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:51 -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 megadepth package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/megadepth.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 1079/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| megadepth 1.4.0 (landing page) David Zhang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: megadepth |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:megadepth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings megadepth_1.4.0.tar.gz |
| StartedAt: 2022-04-12 22:24:25 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:27:20 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 175.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: megadepth.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:megadepth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings megadepth_1.4.0.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/megadepth.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 'megadepth/DESCRIPTION' ... OK
* this is package 'megadepth' version '1.4.0'
* 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 'megadepth' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_coverage 5.88 0.53 6.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_coverage 6.76 0.21 7.28
* 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: OK
megadepth.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/megadepth_1.4.0.tar.gz && rm -rf megadepth.buildbin-libdir && mkdir megadepth.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=megadepth.buildbin-libdir megadepth_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL megadepth_1.4.0.zip && rm megadepth_1.4.0.tar.gz megadepth_1.4.0.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
100 158k 100 158k 0 0 312k 0 --:--:-- --:--:-- --:--:-- 312k
100 158k 100 158k 0 0 312k 0 --:--:-- --:--:-- --:--:-- 312k
install for i386
* installing *source* package 'megadepth' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'megadepth'
finding HTML links ... done
bam_to_bigwig html
bam_to_junctions html
get_coverage html
install_megadepth html
megadepth_cmd html
process_junction_table html
read_coverage html
read_junction_table 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 'megadepth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'megadepth' as megadepth_1.4.0.zip
* DONE (megadepth)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'megadepth' successfully unpacked and MD5 sums checked
|
megadepth.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(megadepth)
>
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.2.0
This is not an interactive session, therefore megadepth has been installed temporarily to
C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/megadepth.exe
>
> test_check("megadepth")
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.2.0
Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/test.bam.all.bw
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test3.bam"
WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed.
Read 12 records
# of overlapping pairs: 3
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/test.bam.all.bw
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
>
> proc.time()
user system elapsed
7.50 0.96 15.98
|
megadepth.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(megadepth)
>
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.2.0
This is not an interactive session, therefore megadepth has been installed temporarily to
C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/megadepth.exe
>
> test_check("megadepth")
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.2.0
Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/test.bam.all.bw
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test3.bam"
WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed.
Read 12 records
# of overlapping pairs: 3
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/test.bam.all.bw
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
>
> proc.time()
user system elapsed
6.59 0.79 13.46
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megadepth.Rcheck/examples_i386/megadepth-Ex.timings
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megadepth.Rcheck/examples_x64/megadepth-Ex.timings
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