| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-27 05:50:32 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 503/2195 | 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/site-library --timings DeepBlueR_1.25.1.tar.gz |
| StartedAt: 2023-03-25 00:45:22 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 01:07:42 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 1339.5 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/site-library --timings DeepBlueR_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 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 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 ... NOTE
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 startup messages can be suppressed ... 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
deepblue_enrich_regions_overlap 0.607 3.467 21.313
deepblue_liftover 0.429 0.022 5.668
deepblue_list_in_use 0.428 0.011 8.079
deepblue_select_column 0.385 0.008 5.457
deepblue_list_genes 0.336 0.056 6.425
deepblue_batch_export_results 0.317 0.032 7.686
deepblue_export_bed 0.195 0.030 5.335
* 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
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820637&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=r820638&key=anonymous_key'
Content type 'application/x-bzip2' length 8455 bytes
==================================================
downloaded 8455 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820639&key=anonymous_key'
Content type 'application/x-bzip2' length 8292 bytes
==================================================
downloaded 8292 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820640&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=r820641&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=r820642&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=r820643&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=r820644&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=r820645&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=r820646&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=r820647&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=r820648&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=r820649&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=r820650&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=r820651&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=r820652&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=r820653&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=r820654&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=r820655&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=r820656&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=r820657&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=r820658&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=r820659&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=r820660&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=r820661&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=r820662&key=anonymous_key'
Content type 'application/x-bzip2' length 104 bytes
==================================================
downloaded 104 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820663&key=anonymous_key'
Content type 'application/x-bzip2' length 10234 bytes
==================================================
downloaded 10234 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820664&key=anonymous_key'
Content type 'application/x-bzip2' length 128 bytes
==================================================
downloaded 128 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820665&key=anonymous_key'
Content type 'application/x-bzip2' length 3033 bytes
==================================================
downloaded 3033 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820666&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=r820667&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=r820668&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=r820669&key=anonymous_key'
Content type 'application/x-bzip2' length 111 bytes
==================================================
downloaded 111 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821753&key=anonymous_key'
Content type 'application/x-bzip2' length 15079172 bytes (14.4 MB)
==================================================
downloaded 14.4 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821754&key=anonymous_key'
Content type 'application/x-bzip2' length 8327085 bytes (7.9 MB)
==================================================
downloaded 7.9 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821755&key=anonymous_key'
Content type 'application/x-bzip2' length 7973306 bytes (7.6 MB)
==================================================
downloaded 7.6 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821756&key=anonymous_key'
Content type 'application/x-bzip2' length 8013107 bytes (7.6 MB)
==================================================
downloaded 7.6 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821757&key=anonymous_key'
Content type 'application/x-bzip2' length 4731837 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821758&key=anonymous_key'
Content type 'application/x-bzip2' length 5147119 bytes (4.9 MB)
==================================================
downloaded 4.9 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821759&key=anonymous_key'
Content type 'application/x-bzip2' length 5499846 bytes (5.2 MB)
==================================================
downloaded 5.2 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821760&key=anonymous_key'
Content type 'application/x-bzip2' length 5326394 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821761&key=anonymous_key'
Content type 'application/x-bzip2' length 6134065 bytes (5.8 MB)
==================================================
downloaded 5.8 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821762&key=anonymous_key'
Content type 'application/x-bzip2' length 4054285 bytes (3.9 MB)
==================================================
downloaded 3.9 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821763&key=anonymous_key'
Content type 'application/x-bzip2' length 4204749 bytes (4.0 MB)
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downloaded 4.0 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821764&key=anonymous_key'
Content type 'application/x-bzip2' length 14120632 bytes (13.5 MB)
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downloaded 13.5 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821765&key=anonymous_key'
Content type 'application/x-bzip2' length 4460643 bytes (4.3 MB)
==================================================
downloaded 4.3 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821766&key=anonymous_key'
Content type 'application/x-bzip2' length 2090953 bytes (2.0 MB)
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downloaded 2.0 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821767&key=anonymous_key'
Content type 'application/x-bzip2' length 2951178 bytes (2.8 MB)
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downloaded 2.8 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821768&key=anonymous_key'
Content type 'application/x-bzip2' length 11178343 bytes (10.7 MB)
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downloaded 10.7 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821769&key=anonymous_key'
Content type 'application/x-bzip2' length 8911337 bytes (8.5 MB)
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trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r821770&key=anonymous_key'
Content type 'application/x-bzip2' length 9794515 bytes (9.3 MB)
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Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
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-devel_2023-03-12_r83975-bin/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)
DeepBlueR.Rcheck/DeepBlueR-Ex.timings
| name | user | system | elapsed | |
| deepblue_aggregate | 0.071 | 0.000 | 2.071 | |
| deepblue_batch_export_results | 0.317 | 0.032 | 7.686 | |
| deepblue_binning | 0.055 | 0.020 | 2.283 | |
| deepblue_cache_status | 0.000 | 0.003 | 0.002 | |
| deepblue_cancel_request | 0.013 | 0.001 | 0.675 | |
| deepblue_chromosomes | 0.056 | 0.004 | 0.733 | |
| deepblue_clear_cache | 0.002 | 0.000 | 0.001 | |
| deepblue_collection_experiments_count | 0.106 | 0.000 | 1.253 | |
| deepblue_commands | 0.119 | 0.012 | 3.937 | |
| deepblue_count_gene_ontology_terms | 0.105 | 0.012 | 1.466 | |
| deepblue_count_regions | 0.031 | 0.005 | 1.405 | |
| deepblue_coverage | 0.031 | 0.004 | 1.367 | |
| deepblue_delete_request_from_cache | 0.003 | 0.000 | 0.005 | |
| deepblue_diff | 0.118 | 0.032 | 1.542 | |
| deepblue_distinct_column_values | 0.037 | 0.000 | 1.441 | |
| deepblue_download_request_data | 0.172 | 0.020 | 4.141 | |
| deepblue_echo | 0.010 | 0.008 | 0.748 | |
| deepblue_enrich_regions_go_terms | 0.052 | 0.027 | 2.210 | |
| deepblue_enrich_regions_overlap | 0.607 | 3.467 | 21.313 | |
| deepblue_export_bed | 0.195 | 0.030 | 5.335 | |
| deepblue_export_meta_data | 0.284 | 0.043 | 1.372 | |
| deepblue_export_tab | 0.129 | 0.004 | 2.922 | |
| deepblue_extend | 0.048 | 0.003 | 1.409 | |
| deepblue_extract_ids | 0.001 | 0.000 | 0.000 | |
| deepblue_extract_names | 0.001 | 0.000 | 0.001 | |
| deepblue_faceting_experiments | 0.029 | 0.000 | 1.487 | |
| deepblue_filter_regions | 0.024 | 0.000 | 0.701 | |
| deepblue_find_motif | 0.026 | 0.000 | 0.706 | |
| deepblue_flank | 0.036 | 0.008 | 1.425 | |
| deepblue_get_biosource_children | 0.016 | 0.002 | 0.697 | |
| deepblue_get_biosource_parents | 0.010 | 0.005 | 0.717 | |
| deepblue_get_biosource_related | 0.014 | 0.003 | 0.708 | |
| deepblue_get_biosource_synonyms | 0.016 | 0.000 | 0.667 | |
| deepblue_get_experiments_by_query | 0.013 | 0.000 | 0.701 | |
| deepblue_get_regions | 0.034 | 0.000 | 1.396 | |
| deepblue_get_request_data | 0.080 | 0.012 | 3.104 | |
| deepblue_info | 0.034 | 0.001 | 0.709 | |
| deepblue_input_regions | 0.016 | 0.000 | 0.701 | |
| deepblue_intersection | 0.054 | 0.004 | 2.076 | |
| deepblue_is_biosource | 0.015 | 0.000 | 0.717 | |
| deepblue_liftover | 0.429 | 0.022 | 5.668 | |
| deepblue_list_annotations | 0.022 | 0.000 | 0.702 | |
| deepblue_list_biosources | 0.016 | 0.001 | 0.694 | |
| deepblue_list_cached_requests | 0.002 | 0.000 | 0.002 | |
| deepblue_list_column_types | 0.060 | 0.000 | 1.065 | |
| deepblue_list_epigenetic_marks | 0.443 | 0.006 | 4.366 | |
| deepblue_list_experiments | 0.152 | 0.003 | 1.566 | |
| deepblue_list_expressions | 0.136 | 0.004 | 1.474 | |
| deepblue_list_gene_models | 0.022 | 0.000 | 0.681 | |
| deepblue_list_genes | 0.336 | 0.056 | 6.425 | |
| deepblue_list_genomes | 0.005 | 0.012 | 0.702 | |
| deepblue_list_in_use | 0.428 | 0.011 | 8.079 | |
| deepblue_list_projects | 0.020 | 0.000 | 0.698 | |
| deepblue_list_recent_experiments | 0.031 | 0.000 | 0.736 | |
| deepblue_list_requests | 0.018 | 0.001 | 0.708 | |
| deepblue_list_samples | 0.138 | 0.008 | 2.579 | |
| deepblue_list_similar_biosources | 0.023 | 0.003 | 0.947 | |
| deepblue_list_similar_epigenetic_marks | 0.019 | 0.009 | 0.729 | |
| deepblue_list_similar_experiments | 0.041 | 0.334 | 1.986 | |
| deepblue_list_similar_genomes | 0.018 | 0.000 | 0.721 | |
| deepblue_list_similar_projects | 0.013 | 0.003 | 0.700 | |
| deepblue_list_similar_techniques | 0.015 | 0.003 | 0.693 | |
| deepblue_list_techniques | 0.026 | 0.001 | 0.724 | |
| deepblue_merge_queries | 0.058 | 0.000 | 2.119 | |
| deepblue_meta_data_to_table | 0.388 | 0.055 | 2.096 | |
| deepblue_name_to_id | 0.048 | 0.001 | 2.092 | |
| deepblue_overlap | 0.056 | 0.006 | 2.117 | |
| deepblue_preview_experiment | 0.015 | 0.000 | 0.699 | |
| deepblue_query_cache | 0.076 | 0.001 | 2.824 | |
| deepblue_query_experiment_type | 0.042 | 0.004 | 1.436 | |
| deepblue_reset_options | 0.001 | 0.000 | 0.000 | |
| deepblue_score_matrix | 0.038 | 0.003 | 1.483 | |
| deepblue_search | 0.041 | 0.003 | 1.068 | |
| deepblue_select_annotations | 0.023 | 0.000 | 1.701 | |
| deepblue_select_column | 0.385 | 0.008 | 5.457 | |
| deepblue_select_experiments | 0.018 | 0.003 | 0.713 | |
| deepblue_select_expressions | 0.024 | 0.000 | 0.702 | |
| deepblue_select_genes | 0.023 | 0.000 | 0.728 | |
| deepblue_select_regions | 0.027 | 0.000 | 0.692 | |
| deepblue_tiling_regions | 0.019 | 0.000 | 0.682 | |