Ying Hu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/OmicCircos |
| Branch: RELEASE_3_9 |
| Last Commit: 0fe9c9e |
| Last Changed Date: 2019-05-02 11:53:43 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:10 -0400 (Wed, 16 Oct 2019).
| Package 1129/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OmicCircos 1.22.0 Ying Hu
| 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: OmicCircos |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicCircos.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmicCircos_1.22.0.tar.gz |
| StartedAt: 2019-10-16 05:41:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:43:03 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 114.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmicCircos.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicCircos.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmicCircos_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/OmicCircos.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicCircos/DESCRIPTION' ... OK
* this is package 'OmicCircos' version '1.22.0'
* 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 'OmicCircos' 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 ... NOTE
circos: no visible global function definition for 'rainbow'
circos: no visible global function definition for 'start'
circos: no visible global function definition for 'end'
circos: no visible global function definition for 'dist'
circos: no visible global function definition for 'hclust'
circos: no visible global function definition for 'colorRampPalette'
circos: no visible global function definition for 'na.omit'
circos: no visible binding for global variable 'quantile'
circos : get.conf.int: no visible global function definition for
't.test'
circos : var1: no visible global function definition for 'var'
circos: no visible global function definition for 'var'
circos : sd1: no visible global function definition for 'sd'
circos: no visible global function definition for 'sd'
circos: no visible global function definition for 'median'
color.bar: no visible global function definition for 'colorRampPalette'
color.bar: no visible global function definition for 'rect'
color.bar: no visible global function definition for 'text'
color.bar: no visible global function definition for 'segments'
do.scale: no visible global function definition for 'segments'
do.scale: no visible global function definition for 'text'
draw.arc.pg: no visible global function definition for 'polygon'
draw.arc.s: no visible global function definition for 'lines'
draw.line: no visible global function definition for 'segments'
draw.line2: no visible global function definition for 'segments'
draw.line3: no visible global function definition for 'segments'
draw.link: no visible global function definition for 'points'
draw.link.pg: no visible global function definition for 'polygon'
draw.link2: no visible global function definition for 'points'
draw.point.w: no visible global function definition for 'points'
draw.text.rt: no visible global function definition for 'text'
draw.text.w: no visible global function definition for 'text'
heatmap.cluster: no visible global function definition for 'dist'
heatmap.cluster: no visible global function definition for 'hclust'
heatmap.cluster: no visible global function definition for 'segments'
heatmap.cluster: no visible global function definition for 'text'
sim.circos: no visible global function definition for 'rnorm'
segAnglePo,GRanges: no visible global function definition for 'start'
segAnglePo,GRanges: no visible global function definition for 'end'
segAnglePo,GRanges: no visible global function definition for 'strand'
segAnglePo,GRanges: no visible binding for global variable 'seg'
segAnglePo,GRanges: no visible binding for global variable
'angle.start'
segAnglePo,GRanges: no visible binding for global variable 'angle.end'
Undefined global functions or variables:
angle.end angle.start colorRampPalette dist end hclust lines median
na.omit points polygon quantile rainbow rect rnorm sd seg segments
start strand t.test text var
Consider adding
importFrom("grDevices", "colorRampPalette", "rainbow")
importFrom("graphics", "lines", "points", "polygon", "rect",
"segments", "text")
importFrom("stats", "dist", "end", "hclust", "median", "na.omit",
"quantile", "rnorm", "sd", "start", "t.test", "var")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/OmicCircos.Rcheck/00check.log'
for details.
OmicCircos.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/OmicCircos_1.22.0.tar.gz && rm -rf OmicCircos.buildbin-libdir && mkdir OmicCircos.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmicCircos.buildbin-libdir OmicCircos_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OmicCircos_1.22.0.zip && rm OmicCircos_1.22.0.tar.gz OmicCircos_1.22.0.zip
###
##############################################################################
##############################################################################
% 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 111k 100 111k 0 0 757k 0 --:--:-- --:--:-- --:--:-- 785k
install for i386
* installing *source* package 'OmicCircos' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'OmicCircos'
finding HTML links ... done
OmicCircos html
TCGA.BC.cnv.2k.60 html
TCGA.BC.fus html
TCGA.BC.gene.exp.2k.60 html
TCGA.BC.sample60 html
TCGA.BC_Her2_cnv_exp html
TCGA.PAM50_genefu_hg18 html
UCSC.chr.colors html
UCSC.hg18 html
UCSC.hg18.chr html
UCSC.hg19 html
UCSC.hg19.chr html
UCSC.mm10 html
UCSC.mm10.chr html
UCSC.mm9 html
UCSC.mm9.chr html
circos html
segAnglePo-methods html
segAnglePo html
sim.circos 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 'OmicCircos' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicCircos' as OmicCircos_1.22.0.zip
* DONE (OmicCircos)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'OmicCircos' successfully unpacked and MD5 sums checked
|
OmicCircos.Rcheck/examples_i386/OmicCircos-Ex.timings
|
OmicCircos.Rcheck/examples_x64/OmicCircos-Ex.timings
|