| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:23 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the slinky package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slinky.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1790/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| slinky 1.10.2 (landing page) Eric Kort
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: slinky |
| Version: 1.10.2 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:slinky.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings slinky_1.10.2.tar.gz |
| StartedAt: 2021-10-15 05:51:53 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:58:20 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 386.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: slinky.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:slinky.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings slinky_1.10.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'slinky/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'slinky' version '1.10.2'
* 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 whether package 'slinky' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'slinky-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clue
> ### Title: clue
> ### Aliases: clue clue,Slinky-method
>
> ### ** Examples
>
> # for build/demo only. You MUST use your own key when using the slinky
> # package.
> user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
+ as='parsed')$user_key
> sl <- Slinky(user_key,
+ system.file('extdata', 'demo.gctx',
+ package='slinky'),
+ system.file('extdata', 'demo_inst_info.txt',
+ package = 'slinky'))
> amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
+ "cell_id" = "MCF7",
+ "is_gold" = TRUE))
Error: Problem with `mutate()` column `distil_id`.
i `distil_id = strsplit(distil_id, "\\|")`.
x non-character argument
Backtrace:
x
1. +-slinky::clue(...)
2. +-slinky::clue(...)
3. | \-dat %>% mutate(distil_id = strsplit(distil_id, "\\|")) %>% unnest(distil_id)
4. +-tidyr::unnest(., distil_id)
5. +-dplyr::mutate(., distil_id = strsplit(distil_id, "\\|"))
6. +-dplyr:::mutate.data.frame(...)
7. | \-dplyr:::mutate_cols(.data, ..., caller_env = caller_env())
8. | +-base::withCallingHandlers(...)
9. | \-mask$eval_all_mutate(quo)
10. +-base::strsplit(distil_id, "\\|")
11. \-base::.handleSimpleError(...)
12. \-dplyr:::h(simpleError(msg, call))
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'slinky-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clue
> ### Title: clue
> ### Aliases: clue clue,Slinky-method
>
> ### ** Examples
>
> # for build/demo only. You MUST use your own key when using the slinky
> # package.
> user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
+ as='parsed')$user_key
> sl <- Slinky(user_key,
+ system.file('extdata', 'demo.gctx',
+ package='slinky'),
+ system.file('extdata', 'demo_inst_info.txt',
+ package = 'slinky'))
> amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
+ "cell_id" = "MCF7",
+ "is_gold" = TRUE))
Error: Problem with `mutate()` column `distil_id`.
i `distil_id = strsplit(distil_id, "\\|")`.
x non-character argument
Backtrace:
x
1. +-slinky::clue(...)
2. +-slinky::clue(...)
3. | \-dat %>% mutate(distil_id = strsplit(distil_id, "\\|")) %>% unnest(distil_id)
4. +-tidyr::unnest(., distil_id)
5. +-dplyr::mutate(., distil_id = strsplit(distil_id, "\\|"))
6. +-dplyr:::mutate.data.frame(...)
7. | \-dplyr:::mutate_cols(.data, ..., caller_env = caller_env())
8. | +-base::withCallingHandlers(...)
9. | \-mask$eval_all_mutate(quo)
10. +-base::strsplit(distil_id, "\\|")
11. \-base::.handleSimpleError(...)
12. \-dplyr:::h(simpleError(msg, call))
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
> library(testthat)
> library(slinky)
>
> test_check("slinky")
== Failed tests ================================================================
-- Failure (test_clue.R:17:3): A gene can be retrieved -------------------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
-- Failure (test_clue.R:22:3): Limit working correctly on genes API ------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
> library(testthat)
> library(slinky)
>
> test_check("slinky")
== Failed tests ================================================================
-- Failure (test_clue.R:17:3): A gene can be retrieved -------------------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
-- Failure (test_clue.R:22:3): Limit working correctly on genes API ------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
Error: Test failures
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: 4 ERRORs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck/00check.log'
for details.
slinky.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/slinky_1.10.2.tar.gz && rm -rf slinky.buildbin-libdir && mkdir slinky.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=slinky.buildbin-libdir slinky_1.10.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL slinky_1.10.2.zip && rm slinky_1.10.2.tar.gz slinky_1.10.2.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
4 1171k 4 51235 0 0 306k 0 0:00:03 --:--:-- 0:00:03 306k
100 1171k 100 1171k 0 0 1458k 0 --:--:-- --:--:-- --:--:-- 1458k
install for i386
* installing *source* package 'slinky' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'slinky'
finding HTML links ... done
Slinky-class html
chDir html
closeAll html
clue html
clueCount html
clueInstances html
clueVehicle html
coerce html
colnames html
controls html
diffexp html
download html
get_metadata html
ks html
loadL1K html
finding level-2 HTML links ... done
metadata html
nrow html
readGCTX html
rownames html
rzs html
slinky-internal html
subset 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 'slinky' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'slinky' as slinky_1.10.2.zip
* DONE (slinky)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'slinky' successfully unpacked and MD5 sums checked
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slinky.Rcheck/tests_i386/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(slinky)
>
> test_check("slinky")
== Failed tests ================================================================
-- Failure (test_clue.R:17:3): A gene can be retrieved -------------------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
-- Failure (test_clue.R:22:3): Limit working correctly on genes API ------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted
|
slinky.Rcheck/tests_x64/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(slinky)
>
> test_check("slinky")
== Failed tests ================================================================
-- Failure (test_clue.R:17:3): A gene can be retrieved -------------------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
-- Failure (test_clue.R:22:3): Limit working correctly on genes API ------------
nrow(tt) not equal to 1.
target is NULL, current is numeric
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted
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slinky.Rcheck/examples_i386/slinky-Ex.timings
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slinky.Rcheck/examples_x64/slinky-Ex.timings
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