| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-29 16:33:43 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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 DeepBlueR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeepBlueR.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 485/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeepBlueR 1.25.1 (landing page) Felipe Albrecht
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DeepBlueR |
| Version: 1.25.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DeepBlueR_1.25.1.tar.gz |
| StartedAt: 2023-01-28 21:07:50 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 21:21:51 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 841.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DeepBlueR_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.25.1’
* 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 ‘DeepBlueR’ can be installed ... 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'DeepBlueR' was found
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
v0.99.0 Initial Bioconductor submission
Cannot process chunk/lines:
v1.0.0 Bioconductor 3.4 release
Cannot process chunk/lines:
v1.2.0 Bioconductor 3.5 release
Cannot process chunk/lines:
v1.4.0 Bioconductor 3.6 release
Cannot process chunk/lines:
v1.4.1 Bugfixes following changes in the DeepBlue API
* 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 loading without being on the library search path ... WARNING
Error in library(DeepBlueR, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘DeepBlueR’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... NOTE
prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples
* 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 ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘DeepBlueR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘DeepBlueR.Rmd’ using rmarkdown
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820591&key=anonymous_key'
Content type 'application/x-bzip2' length 45606 bytes (44 KB)
==================================================
downloaded 44 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726035&key=anonymous_key'
Content type 'application/x-bzip2' length 1394381 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820593&key=anonymous_key'
Content type 'application/x-bzip2' length 2618 bytes
==================================================
downloaded 2618 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820594&key=anonymous_key'
Content type 'application/x-bzip2' length 8189 bytes
==================================================
downloaded 8189 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726036&key=anonymous_key'
Content type 'application/x-bzip2' length 21187 bytes (20 KB)
==================================================
downloaded 20 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726037&key=anonymous_key'
Content type 'application/x-bzip2' length 171602 bytes (167 KB)
==================================================
downloaded 167 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726038&key=anonymous_key'
Content type 'application/x-bzip2' length 7420781 bytes (7.1 MB)
==================================================
downloaded 7.1 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726039&key=anonymous_key'
Content type 'application/x-bzip2' length 14872 bytes (14 KB)
==================================================
downloaded 14 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726040&key=anonymous_key'
Content type 'application/x-bzip2' length 2048 bytes
==================================================
downloaded 2048 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726042&key=anonymous_key'
Content type 'application/x-bzip2' length 18557 bytes (18 KB)
==================================================
downloaded 18 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726043&key=anonymous_key'
Content type 'application/x-bzip2' length 271 bytes
==================================================
downloaded 271 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726044&key=anonymous_key'
Content type 'application/x-bzip2' length 32905 bytes (32 KB)
==================================================
downloaded 32 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820603&key=anonymous_key'
Content type 'application/x-bzip2' length 1776 bytes
==================================================
downloaded 1776 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820604&key=anonymous_key'
Content type 'application/x-bzip2' length 12681 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820605&key=anonymous_key'
Content type 'application/x-bzip2' length 8617 bytes
==================================================
downloaded 8617 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820606&key=anonymous_key'
Content type 'application/x-bzip2' length 8502 bytes
==================================================
downloaded 8502 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820607&key=anonymous_key'
Content type 'application/x-bzip2' length 7612 bytes
==================================================
downloaded 7612 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820608&key=anonymous_key'
Content type 'application/x-bzip2' length 7791 bytes
==================================================
downloaded 7791 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820609&key=anonymous_key'
Content type 'application/x-bzip2' length 7772 bytes
==================================================
downloaded 7772 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820610&key=anonymous_key'
Content type 'application/x-bzip2' length 6613 bytes
==================================================
downloaded 6613 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820611&key=anonymous_key'
Content type 'application/x-bzip2' length 6189 bytes
==================================================
downloaded 6189 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820612&key=anonymous_key'
Content type 'application/x-bzip2' length 6516 bytes
==================================================
downloaded 6516 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820613&key=anonymous_key'
Content type 'application/x-bzip2' length 5784 bytes
==================================================
downloaded 5784 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820614&key=anonymous_key'
Content type 'application/x-bzip2' length 4324 bytes
==================================================
downloaded 4324 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820615&key=anonymous_key'
Content type 'application/x-bzip2' length 113 bytes
==================================================
downloaded 113 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820616&key=anonymous_key'
Content type 'application/x-bzip2' length 121 bytes
==================================================
downloaded 121 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820617&key=anonymous_key'
Content type 'application/x-bzip2' length 113 bytes
==================================================
downloaded 113 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820618&key=anonymous_key'
Content type 'application/x-bzip2' length 76 bytes
==================================================
downloaded 76 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820619&key=anonymous_key'
Content type 'application/x-bzip2' length 121 bytes
==================================================
downloaded 121 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820620&key=anonymous_key'
Content type 'application/x-bzip2' length 12450 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820621&key=anonymous_key'
Content type 'application/x-bzip2' length 10112 bytes
==================================================
downloaded 10112 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820622&key=anonymous_key'
Content type 'application/x-bzip2' length 10467 bytes (10 KB)
==================================================
downloaded 10 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820623&key=anonymous_key'
Content type 'application/x-bzip2' length 76 bytes
==================================================
downloaded 76 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820624&key=anonymous_key'
Content type 'application/x-bzip2' length 125 bytes
==================================================
downloaded 125 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820625&key=anonymous_key'
Content type 'application/x-bzip2' length 76 bytes
==================================================
downloaded 76 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820626&key=anonymous_key'
Content type 'application/x-bzip2' length 122 bytes
==================================================
downloaded 122 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820627&key=anonymous_key'
Content type 'application/x-bzip2' length 112 bytes
==================================================
downloaded 112 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820628&key=anonymous_key'
Content type 'application/x-bzip2' length 76 bytes
==================================================
downloaded 76 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820629&key=anonymous_key'
Content type 'application/x-bzip2' length 10165 bytes
==================================================
downloaded 10165 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820630&key=anonymous_key'
Content type 'application/x-bzip2' length 112 bytes
==================================================
downloaded 112 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820631&key=anonymous_key'
Content type 'application/x-bzip2' length 112 bytes
==================================================
downloaded 112 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820632&key=anonymous_key'
Content type 'application/x-bzip2' length 121 bytes
==================================================
downloaded 121 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820633&key=anonymous_key'
Content type 'application/x-bzip2' length 112 bytes
==================================================
downloaded 112 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820634&key=anonymous_key'
Content type 'application/x-bzip2' length 169 bytes
==================================================
downloaded 169 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820635&key=anonymous_key'
Content type 'application/x-bzip2' length 9849 bytes
==================================================
downloaded 9849 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820636&key=anonymous_key'
Content type 'application/x-bzip2' length 9703 bytes
==================================================
downloaded 9703 bytes
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.
DeepBlueR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DeepBlueR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘DeepBlueR’ ... ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading Called method: deepblue_list_column_types Reported status was: okay Called method: deepblue_info Reported status was: okay ** 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 (DeepBlueR)