Steffi Grote
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ABAEnrichment |
| Branch: RELEASE_3_9 |
| Last Commit: e1ebfb5 |
| Last Changed Date: 2019-07-14 10:14:59 -0400 (Sun, 14 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:07:17 -0400 (Wed, 16 Oct 2019).
| Package 7/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ABAEnrichment 1.14.1 Steffi Grote
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ABAEnrichment |
| Version: 1.14.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ABAEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ABAEnrichment_1.14.1.tar.gz |
| StartedAt: 2019-10-15 23:37:33 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 23:39:27 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 113.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ABAEnrichment.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ABAEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ABAEnrichment_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ABAEnrichment.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABAEnrichment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ABAEnrichment’ version ‘1.14.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ABAEnrichment’ 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 ... NOTE
aba_enrich: no visible binding for global variable ‘signal’
aba_enrich: no visible binding for global variable ‘gene_id’
get_annotated_genes: no visible binding for global variable ‘signal’
get_annotated_genes: no visible binding for global variable ‘gene_id’
get_annotated_genes: no visible binding for global variable
‘structure_id’
Undefined global functions or variables:
gene_id signal structure_id
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
aba_enrich 11.400 0.423 10.462
get_annotated_genes 9.493 0.236 5.105
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/ABAEnrichment.Rcheck/00check.log’
for details.
ABAEnrichment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ABAEnrichment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘ABAEnrichment’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c unlock_environment.cc -o unlock_environment.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o ABAEnrichment.so RcppExports.o unlock_environment.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-ABAEnrichment/00new/ABAEnrichment/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ABAEnrichment)
ABAEnrichment.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(ABAEnrichment)
>
> test_check("ABAEnrichment")
V1 V2 V3
2 chr3 76500000 90500000
3 chr7 113600000 124700000
1 chr1 104000000 114900000
4 chr8 54500000 65400000
V1 V2 V3
1 chr1 104000000 114900000
2 chr3 76500000 90500000
3 chr5 0 4700000
4 chr7 113600000 124700000
5 chr8 54500000 65400000
Read 1535 terms.
Found 1534 nodes.
Graph created.
Reading nodes_per_gene file...
Found 188 usable entrys in /tmp/Rtmp32RFoT/file292165b8df3a_Allen:4005 with 678 GOs
Creating 1000 random gene sets from 4 random regions...
The candidate does not fit - try again...
This was trial 1
The candidate does not fit - try again...
This was trial 2
The candidate does not fit - try again...
This was trial 3
The candidate does not fit - try again...
This was trial 4
The candidate does not fit - try again...
This was trial 5
The candidate does not fit - try again...
This was trial 6
The candidate does not fit - try again...
This was trial 7
The candidate does not fit - try again...
This was trial 8
The candidate does not fit - try again...
This was trial 9
The candidate does not fit - try again...
This was trial 10
Error: 10 times in a row the candidate regions could not be placed randomly without forcing them to overlap. Consider using larger background regions.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 146 | SKIPPED: 0 | WARNINGS: 49 | FAILED: 0 ]
>
> proc.time()
user system elapsed
72.151 3.092 59.081
ABAEnrichment.Rcheck/ABAEnrichment-Ex.timings
| name | user | system | elapsed | |
| aba_enrich | 11.400 | 0.423 | 10.462 | |
| get_annotated_genes | 9.493 | 0.236 | 5.105 | |
| get_expression | 0.083 | 0.037 | 0.120 | |
| get_id | 0.013 | 0.001 | 0.014 | |
| get_name | 0.002 | 0.001 | 0.004 | |
| get_sampled_substructures | 0.002 | 0.000 | 0.002 | |
| get_superstructures | 0.032 | 0.004 | 0.036 | |
| plot_expression | 0.132 | 0.024 | 0.154 | |