| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:37 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1111/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| megadepth 1.9.0 (landing page) David Zhang
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: megadepth |
| Version: 1.9.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:megadepth.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings megadepth_1.9.0.tar.gz |
| StartedAt: 2022-12-29 01:07:58 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:09:33 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 95.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: megadepth.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:megadepth.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings megadepth_1.9.0.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/megadepth.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'megadepth/DESCRIPTION' ... OK
* this is package 'megadepth' version '1.9.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_coverage 5.39 0.38 6.05
* 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: OK
megadepth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL megadepth ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'megadepth' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (megadepth)
megadepth.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpUZj9qL/megadepth.exe
>
> test_check("megadepth")
Processing BAM: "F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.17-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 F:/biocbuild/bbs-3.17-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 F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.2.0
Processing F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpUZj9qL/test.bam.all.bw
Processing BAM: "F:/biocbuild/bbs-3.17-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 F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpUZj9qL/test.bam.all.bw
Processing BAM: "F:/biocbuild/bbs-3.17-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.17-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
3.96 0.85 12.35
megadepth.Rcheck/megadepth-Ex.timings
| name | user | system | elapsed | |
| bam_to_bigwig | 0.03 | 0.03 | 0.64 | |
| bam_to_junctions | 0.56 | 0.12 | 0.92 | |
| get_coverage | 5.39 | 0.38 | 6.05 | |
| install_megadepth | 0.00 | 0.01 | 0.46 | |
| megadepth_cmd | 0.11 | 0.11 | 1.73 | |
| process_junction_table | 0.19 | 0.11 | 0.66 | |
| read_coverage | 0.29 | 0.14 | 0.89 | |
| read_junction_table | 0.18 | 0.11 | 0.86 | |