Phaedra Agius
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/SCANVIS |
| git_branch: RELEASE_3_14 |
| git_last_commit: d49015e |
| git_last_commit_date: 2021-10-26 12:53:04 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:18 -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 SCANVIS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCANVIS.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 1707/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SCANVIS 1.8.0 (landing page) Phaedra Agius
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SCANVIS |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCANVIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SCANVIS_1.8.0.tar.gz |
| StartedAt: 2022-04-13 02:18:02 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:22:15 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 253.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SCANVIS.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCANVIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SCANVIS_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SCANVIS.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 'SCANVIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SCANVIS' version '1.8.0'
* 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 'SCANVIS' 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
SCANVISannotation: no visible global function definition for
'download.file'
SCANVISannotation: no visible binding for global variable 'out.dir'
SCANVISannotation: no visible global function definition for
'elementMetadata'
SCANVISannotation: no visible global function definition for 'seqnames'
SCANVISmerge: no visible global function definition for 'read.delim'
SCANVISread_STAR: no visible global function definition for
'read.delim'
SCANVISscan: no visible global function definition for 'read.delim'
SCANVISscan: no visible global function definition for 'tail'
SCANVISscan: no visible global function definition for 'write.table'
SCANVISvisual: no visible global function definition for 'rect'
SCANVISvisual: no visible global function definition for 'lines'
SCANVISvisual: no visible global function definition for 'text'
SCANVISvisual: no visible global function definition for 'legend'
SCANVISvisual: no visible global function definition for 'write.table'
SCANVISvisual: no visible global function definition for 'read.delim'
SCANVISvisual: no visible global function definition for 'tail'
SCANVISvisual: no visible global function definition for 'head'
SCANVISvisual: no visible global function definition for 'points'
gene2roi: no visible global function definition for 'tail'
Undefined global functions or variables:
download.file elementMetadata head legend lines out.dir points
read.delim rect seqnames tail text write.table
Consider adding
importFrom("graphics", "legend", "lines", "points", "rect", "text")
importFrom("utils", "download.file", "head", "read.delim", "tail",
"write.table")
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' ... ERROR
Running examples in 'SCANVIS-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ls_url
> ### Title: list files available at annotation/gencode url
> ### Aliases: ls_url
> ### Keywords: gencode annotation GTF
>
> ### ** Examples
>
> ftpfiles=ls_url('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/')
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/
Error in ls_url("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/") :
url.exists(url) is not TRUE
Calls: ls_url -> stopifnot
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SCANVIS-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ls_url
> ### Title: list files available at annotation/gencode url
> ### Aliases: ls_url
> ### Keywords: gencode annotation GTF
>
> ### ** Examples
>
> ftpfiles=ls_url('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/')
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/
Error in ls_url("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/") :
url.exists(url) is not TRUE
Calls: ls_url -> stopifnot
Execution halted
* 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 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/SCANVIS.Rcheck/00check.log'
for details.
SCANVIS.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/SCANVIS_1.8.0.tar.gz && rm -rf SCANVIS.buildbin-libdir && mkdir SCANVIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCANVIS.buildbin-libdir SCANVIS_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SCANVIS_1.8.0.zip && rm SCANVIS_1.8.0.tar.gz SCANVIS_1.8.0.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 276k 100 276k 0 0 822k 0 --:--:-- --:--:-- --:--:-- 824k
install for i386
* installing *source* package 'SCANVIS' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SCANVIS'
finding HTML links ... done
GBM html
IR2Mat html
LUAD html
LUSC html
SCANVIS-package html
SCANVISannotation html
SCANVISexamples html
SCANVISlinkvar html
SCANVISmerge html
SCANVISreadSTAR html
SCANVISscan html
SCANVISvisual html
gbm3 html
gbm3.vcf html
gen19 html
gene2roi html
ls_url 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 'SCANVIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SCANVIS' as SCANVIS_1.8.0.zip
* DONE (SCANVIS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SCANVIS' successfully unpacked and MD5 sums checked
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SCANVIS.Rcheck/examples_i386/SCANVIS-Ex.timings
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SCANVIS.Rcheck/examples_x64/SCANVIS-Ex.timings
|