Bohdan Khomtchouk
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/geneXtendeR |
| Branch: RELEASE_3_9 |
| Last Commit: 4554972 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:09:45 -0400 (Wed, 16 Oct 2019).
| Package 645/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| geneXtendeR 1.10.0 Bohdan Khomtchouk
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| 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: geneXtendeR |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings geneXtendeR_1.10.0.tar.gz |
| StartedAt: 2019-10-16 01:52:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:17:33 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1478.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: geneXtendeR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings geneXtendeR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.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 ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘geneXtendeR’ can be installed ... WARNING
Found the following significant warnings:
annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
data 5.8Mb
doc 1.9Mb
extdata 3.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘rtracklayer’
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
* 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
Namespaces in Imports field not imported from:
‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.geneXtender: no visible binding for global variable ‘type’
.geneXtender: no visible binding for global variable ‘seqid’
.geneXtender: no visible binding for global variable ‘gene_id’
.geneXtender: no visible binding for global variable ‘gene_name’
annotate_n: no visible binding for global variable ‘..I’
annotate_n: no visible binding for global variable ‘seqid’
diffGO: no visible binding for global variable ‘rat’
gene_annotate: no visible global function definition for ‘.’
gene_annotate: no visible binding for global variable
‘Distance-of-Gene-to-Nearest-Peak’
gene_annotate: no visible global function definition for ‘sd’
gene_annotate: no visible binding for global variable ‘Chromosome’
gene_annotate: no visible binding for global variable ‘Gene-Start’
gene_annotate: no visible binding for global variable ‘Gene-End’
gene_annotate: no visible binding for global variable ‘Gene-ID’
gene_annotate: no visible binding for global variable ‘Gene-Name’
gene_annotate: no visible binding for global variable
‘Peaks-on-Gene-Body’
gene_annotate: no visible binding for global variable
‘Number-of-Peaks-Associated-with-Gene’
gene_lookup: no visible binding for global variable ‘gene_name_id’
gene_lookup: no visible binding for global variable ‘gene_id’
gene_lookup : internal_find: no visible binding for global variable
‘Chromosome’
gene_lookup : internal_find: no visible binding for global variable
‘distance’
gene_lookup : internal_find: no visible global function definition for
‘na.omit’
gene_lookup: no visible binding for global variable ‘..I’
gene_lookup: no visible binding for global variable ‘distance’
makeWordCloud: no visible binding for global variable ‘rat’
meanPeakLength: no visible binding for global variable ‘rat’
peaksInput: no visible binding for global variable ‘chr’
peaksInput: no visible global function definition for ‘na.omit’
peaksMerge: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘g’
peaksMerge: no visible global function definition for ‘.’
plotWordFreq : geneXtender: no visible binding for global variable
‘type’
plotWordFreq : geneXtender: no visible binding for global variable
‘seqid’
plotWordFreq : geneXtender: no visible binding for global variable
‘gene_id’
plotWordFreq : geneXtender: no visible binding for global variable
‘gene_name’
Undefined global functions or variables:
. ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID
Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene
Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id
na.omit rat sd seqid type
Consider adding
importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
‘vignettes/geneXtendeR.Rnw’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meanPeakLengthPlot 53.654 0.324 53.464
hotspotPlot 37.531 0.300 32.644
barChart 29.240 0.226 28.506
annotate 26.523 0.371 27.859
cumlinePlot 25.317 0.293 27.952
linePlot 24.623 0.208 24.642
plotWordFreq 24.071 0.412 23.526
diffGO 22.575 0.291 22.822
peakLengthBoxplot 22.105 0.124 21.133
gene_annotate 20.866 0.258 21.360
meanPeakLength 20.688 0.149 18.766
makeNetwork 20.574 0.248 20.232
makeWordCloud 20.263 0.169 19.427
distinct 19.384 0.168 20.230
gene_lookup 13.291 0.089 14.205
peaksInput 5.742 0.118 1.634
peaksMerge 5.360 0.058 1.398
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.
geneXtendeR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL geneXtendeR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(varstr, 50000, varfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(vcfstr, 10000, vcffp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c extract_number.c -o extract_number.o
extract_number.c: In function ‘extractnumber’:
extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable]
long n_1;
^~~
extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable]
long j_1;
^~~
extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable]
char * pvcfcol5_5;
^~~~~~~~~~
extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable]
char * pvcfcol4_4;
^~~~~~~~~~
extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable]
char * pvcfcol3_3;
^~~~~~~~~~
extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable]
char * pvcfcol2_2;
^~~~~~~~~~
extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable]
char * pvcfcol1_1;
^~~~~~~~~~
extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(varstr, 50000, varfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(vcfstr, 10000, vcffp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c extract_peaks.c -o extract_peaks.o
extract_peaks.c: In function ‘extractpeaks’:
extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(varstr, 50000, varfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(vcfstr, 10000, vcffp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-geneXtendeR/00new/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (geneXtendeR)
geneXtendeR.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(geneXtendeR)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GO.db
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")'.
>
> test_check("geneXtendeR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 86 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
4003.379 19.597 832.523
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
| name | user | system | elapsed | |
| allPeakLengths | 0.031 | 0.000 | 0.043 | |
| annotate | 26.523 | 0.371 | 27.859 | |
| annotate_n | 0.001 | 0.000 | 0.000 | |
| barChart | 29.240 | 0.226 | 28.506 | |
| cumlinePlot | 25.317 | 0.293 | 27.952 | |
| diffGO | 22.575 | 0.291 | 22.822 | |
| distinct | 19.384 | 0.168 | 20.230 | |
| gene_annotate | 20.866 | 0.258 | 21.360 | |
| gene_lookup | 13.291 | 0.089 | 14.205 | |
| hotspotPlot | 37.531 | 0.300 | 32.644 | |
| linePlot | 24.623 | 0.208 | 24.642 | |
| makeNetwork | 20.574 | 0.248 | 20.232 | |
| makeWordCloud | 20.263 | 0.169 | 19.427 | |
| meanPeakLength | 20.688 | 0.149 | 18.766 | |
| meanPeakLengthPlot | 53.654 | 0.324 | 53.464 | |
| peakLengthBoxplot | 22.105 | 0.124 | 21.133 | |
| peaksInput | 5.742 | 0.118 | 1.634 | |
| peaksMerge | 5.360 | 0.058 | 1.398 | |
| plotWordFreq | 24.071 | 0.412 | 23.526 | |
| rat | 4.262 | 0.188 | 4.671 | |
| samplepeaksinput | 0.188 | 0.000 | 0.078 | |