CRAN Failing on r-devel-linux-x86_64-debian-clang #318

elinw · 2019-11-24T23:25:56Z

I have tried to find the closest match on rhub to r-devel-linux-x86_64-debian-clang. I know from experience that the version CRAN uses does not support UTF8. So I have been using rhub debian-clang-devel along with various other debian platforms. When the tests run on rhub they pass, but on CRAN they fail. This seems to be due to UTF8 support (or lack thereof). As of now you can see it here:
https://cran.r-project.org/web/checks/check_results_skimr.html

I know how to fix the issue, but I'm wondering why the tests pass on rhub or if I should be using a different platform.

gaborcsardi · 2019-11-24T23:31:49Z

Can you pls point to the corresponding R-hub build log? Thanks?

elinw · 2019-11-25T02:47:58Z

> check_for_cran(platforms = "debian-gcc-devel")
─  Building package
─  Uploading package
─  Preparing build, see status at
   https://builder.r-hub.io/status/skimr_2.0.1.tar.gz-b130812c9a584627be9e68ae419f5357
─  Build started
─  Downloading and unpacking package file
─  Querying system requirements
─  Installing system requirements
─  Starting Docker container
─  Querying package dependencies
─  Installing package dependencies
─  Running R CMD check
   About to run xvfb-run R CMD check --as-cran skimr_2.0.1.tar.gz
─  using log directory ‘/home/docker/skimr.Rcheck’ (1.9s)
─  using R Under development (unstable) (2019-11-23 r77455)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
─  using option ‘--as-cran’
✔  checking for file ‘skimr/DESCRIPTION’
─  this is package ‘skimr’ version ‘2.0.1’
─  package encoding: UTF-8
─  checking CRAN incoming feasibility ...NB: need Internet access to use CRAN incoming checks (8.9s)
    NOTE
   Maintainer: ‘Elin Waring <elin.waring@gmail.com>’
   
   Possibly mis-spelled words in DESCRIPTION:
     README (34:5)
     skimr (33:56)
✔  checking package namespace information
✔  checking package dependencies (3s)
✔  checking if this is a source package
✔  checking if there is a namespace
✔  checking for executable files
✔  checking for hidden files and directories
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
✔  checking serialization versions
✔  checking whether package ‘skimr’ can be installed (5.8s)
✔  checking installed package size
✔  checking package directory
✔  checking for future file timestamps (1.5s)
✔  checking ‘build’ directory
✔  checking DESCRIPTION meta-information
✔  checking top-level files
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories
✔  checking R files for non-ASCII characters (1.4s)
✔  checking R files for syntax errors
✔  checking whether the package can be loaded
✔  checking whether the package can be loaded with stated dependencies (1.5s)
✔  checking whether the package can be unloaded cleanly
✔  checking whether the namespace can be loaded with stated dependencies (1.4s)
✔  checking whether the namespace can be unloaded cleanly
✔  checking loading without being on the library search path (1.5s)
✔  checking use of S3 registration (3.1s)
✔  checking dependencies in R code (1.3s)
✔  checking S3 generic/method consistency (1.5s)
✔  checking replacement functions (1.4s)
✔  checking foreign function calls
✔  checking R code for possible problems (7.3s)
✔  checking Rd files (1.4s)
✔  checking Rd metadata
✔  checking Rd line widths
✔  checking Rd cross-references
✔  checking for missing documentation entries (1.5s)
✔  checking for code/documentation mismatches (1.4s)
✔  checking Rd \usage sections (3.2s)
✔  checking Rd contents
✔  checking for unstated dependencies in examples
✔  checking installed files from ‘inst/doc’
✔  checking files in ‘vignettes’
✔  checking examples (4.8s)
✔  checking for unstated dependencies in ‘tests’
─  checking tests (1.5s)
✔  Running ‘testthat.R’ [11s/11s] (10.8s)
✔  checking for unstated dependencies in vignettes (10.8s)
✔  checking package vignettes in ‘inst/doc’
✔  checking re-building of vignette outputs (11.9s)
✔  checking PDF version of manual (3.4s)
✔  checking for non-standard things in the check directory
✔  checking for detritus in the temp directory
   
─  Done with R CMD check
─  Saving artifacts

gaborcsardi · 2019-11-25T02:50:43Z

check_for_cran(platforms = "debian-gcc-devel")

The platform that has a non-UTF-8 locale is called debian-clang-devel:

❯ rhub::platforms()
debian-clang-devel:
  Debian Linux, R-devel, clang, ISO-8859-15 locale
[...]

Can you pls try that? Thanks.

elinw · 2019-11-26T13:50:46Z

I actually tried that one previously, but here's the current one:

rhub::check_for_cran(platforms = "debian-gcc-devel")
─ Building package
─ Uploading package
─ Preparing build, see status at
https://builder.r-hub.io/status/skimr_2.0.1.tar.gz-ceb1d509679a4cb0ac6f1192377ee7f5
─ Build started
─ Downloading and unpacking package file
─ Querying system requirements
─ Installing system requirements
─ Starting Docker container
─ Querying package dependencies
─ Installing package dependencies
─ Running R CMD check
About to run xvfb-run R CMD check --as-cran skimr_2.0.1.tar.gz
─ using log directory ‘/home/docker/skimr.Rcheck’
─ using R Under development (unstable) (2019-11-23 r77455)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
─ using option ‘--as-cran’ (1.1s)
✔ checking for file ‘skimr/DESCRIPTION’
─ this is package ‘skimr’ version ‘2.0.1’
─ package encoding: UTF-8
─ checking CRAN incoming feasibility ...NB: need Internet access to use CRAN incoming checks (9.2s)
NOTE
Maintainer: ‘Elin Waring elin.waring@gmail.com’

Possibly mis-spelled words in DESCRIPTION:
README (34:5)
skimr (33:56)
✔ checking package namespace information
✔ checking package dependencies (2.9s)
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for executable files
✔ checking for hidden files and directories
✔ checking for portable file names
✔ checking for sufficient/correct file permissions
✔ checking serialization versions
✔ checking whether package ‘skimr’ can be installed (5.8s)
✔ checking installed package size
✔ checking package directory
✔ checking for future file timestamps (1.1s)
✔ checking ‘build’ directory
✔ checking DESCRIPTION meta-information
✔ checking top-level files
✔ checking for left-over files
✔ checking index information (1.2s)
✔ checking package subdirectories
✔ checking R files for non-ASCII characters
✔ checking R files for syntax errors
✔ checking whether the package can be loaded (1.2s)
✔ checking whether the package can be loaded with stated dependencies (1.6s)
✔ checking whether the package can be unloaded cleanly
✔ checking whether the namespace can be loaded with stated dependencies (1.4s)
✔ checking whether the namespace can be unloaded cleanly
✔ checking loading without being on the library search path (1.2s)
✔ checking use of S3 registration (2.4s)
✔ checking dependencies in R code (972ms)
✔ checking S3 generic/method consistency (2.1s)
✔ checking replacement functions (718ms)
✔ checking foreign function calls (1.5s)
✔ checking R code for possible problems (7.4s)
✔ checking Rd files
✔ checking Rd metadata
✔ checking Rd line widths (715ms)
✔ checking Rd cross-references
✔ checking for missing documentation entries (708ms)
✔ checking for code/documentation mismatches (2.9s)
✔ checking Rd \usage sections (2.4s)
✔ checking Rd contents
✔ checking for unstated dependencies in examples (719ms)
✔ checking installed files from ‘inst/doc’
✔ checking files in ‘vignettes’
✔ checking examples (5.1s)
✔ checking for unstated dependencies in ‘tests’
─ checking tests
✔ Running ‘testthat.R’ [11s/11s] (11.6s)
✔ checking for unstated dependencies in vignettes (12.5s)
✔ checking package vignettes in ‘inst/doc’
✔ checking re-building of vignette outputs (11.7s)
✔ checking PDF version of manual (2.9s)
✔ checking for non-standard things in the check directory
✔ checking for detritus in the temp directory

─ Done with R CMD check
─ Saving artifacts

gaborcsardi · 2019-11-26T13:53:46Z

That seems like debian-gcc-devel again. The correct platform is debian-clang-devel.

elinw · 2019-11-27T00:25:36Z

It's actually totally dying.

rhub::check_for_cran(platforms = "debian-clang-devel")
─ Building package
─ Uploading package
─ Preparing build, see status at
https://builder.r-hub.io/status/skimr_2.0.2.tar.gz-f11f0608c7424a86b43cee4842312b0d
─ Build started
─ Downloading and unpacking package file
─ Querying system requirements
─ Installing system requirements
─ Starting Docker container
─ Querying package dependencies
─ Installing package dependencies

That's it. ... just ends there.

I'm assuming that's a separate issue maybe related to dependencies since CRAN gets to the point of running the tests, which fail.

Here are the dependencies.

Imports:
cli,
crayon,
dplyr (>= 0.8.0),
knitr (>= 1.2),
magrittr (>= 1.5),
purrr,
repr,
rlang (>= 0.3.1),
stats,
stringr (>= 1.1),
tibble (>= 2.0.0),
tidyr (>= 1.0),
tidyselect (>= 0.2.5)
Suggests:
covr,
extrafont,
rmarkdown,
sf,
testthat (>= 2.0.0),
withr

elinw · 2019-11-28T00:37:18Z

Okay I'm sorry for not being a better rhub user but this is what I am seeing in the log.

Error in loadNamespace(name) : there is no package called 'BiocManager'
Calls: options ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error in loadNamespace(name) : there is no package called 'BiocManager'
Calls: options ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Build step 'Execute shell' marked build as failure

HeidiSeibold · 2019-12-10T12:13:52Z

I get the same error, when I run check(platform = "debian-clang-devel", check_args = "--as-cran", show_status = FALSE).

Any idea why there is a problem with BiocManager?

Output

https://builder.r-hub.io/status/original/model4you_0.9-5.tar.gz-324f2dbafa0b4747a67ff4e2d65cefe7

+R-HUB-R-HUB-R-HUBdocker run -i --user docker --env-file /tmp/filerxJotY -v /home/ubuntu/workspace/model4you_0.9-5.tar.gz-324f2dbafa0b4747a67ff4e2d65cefe7/model4you_0.9-5.tar.gz:/tmp/model4you_0.9-5.tar.gz --name model4you_0.9-5.tar.gz-324f2dbafa0b4747a67ff4e2d65cefe7-2 sha256:17e6c5b01ead31dfac2cde2d8f71356664421b0bce5628b6d2bb5d69a6e04832 /bin/bash -l

R Under development (unstable) (2019-08-18 r77026) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

  Natural language support but running in an English locale

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.

> install.packages('BiocManager')
Installing package into '/home/docker/R'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz'
Content type 'application/x-gzip' length 40205 bytes (39 KB)
==================================================
downloaded 39 KB

* installing *source* package 'BiocManager' ...
** package 'BiocManager' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'BiocManager':
 .onAttach failed in attachNamespace() for 'BiocManager', details:
  call: if (version[, 1:2] != version) return(sprintf("version '%s' must have two components, e.g., '3.7'", 
  error: argument is of length zero
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/docker/R/BiocManager'

The downloaded source packages are in
	'/tmp/RtmpO3FrcM/downloaded_packages'
> Warning message:
In install.packages("BiocManager") :
  installation of package 'BiocManager' had non-zero exit status

phargarten2 · 2019-12-12T17:00:09Z

Same for me as well upon running check_for_cran() with the platform argument equalling "debian-clang-devel"

It appears BiocManager could not be installed on this platform.

Here is my full log:

* installing *source* package 'BiocManager' ...
** package 'BiocManager' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'BiocManager':
 .onAttach failed in attachNamespace() for 'BiocManager', details:
  call: if (version[, 1:2] != version) return(sprintf("version '%s' must have two components, e.g., '3.7'", 
  error: argument is of length zero
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/docker/R/BiocManager'

The downloaded source packages are in
	'/tmp/Rtmpe7GFmJ/downloaded_packages'
Warning message:
In install.packages("BiocManager") :
  installation of package 'BiocManager' had non-zero exit status
> 
> 
>>>>>==================== Querying package dependencies
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  114k  100  114k    0     0   294k      0 --:--:-- --:--:-- --:--:--  293k

R Under development (unstable) (2019-08-18 r77026) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

  Natural language support but running in an English locale

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.

Error in loadNamespace(name) : there is no package called 'BiocManager'
Calls: options ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
>>>>>==================== Installing package dependencies
/opt/R-devel/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
clang
clang version 7.0.1-9 (tags/RELEASE_701/final)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
clang++ -std=gnu++11
clang version 7.0.1-9 (tags/RELEASE_701/final)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
Pandoc:
/usr/bin/pandoc
-rwxr-xr-x 1 root root 123361336 Nov 18 18:03 /usr/bin/pandoc
-rwxr-xr-x 1 root root 103868984 Sep 17 03:21 /usr/bin/pandoc-citeproc

R Under development (unstable) (2019-08-18 r77026) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

  Natural language support but running in an English locale

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.

Error in loadNamespace(name) : there is no package called 'BiocManager'
Calls: options ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error in loadNamespace(name) : there is no package called 'BiocManager'
Calls: options ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/miWQS_0.2.0.tar.gz-854557fb42c8438f81d1dcf9a558fd8d/2019-12-12T16:46:36Z
{"status":"ok"}
Finished: FAILURE

elinw · 2020-02-02T03:10:54Z

Currently check_for_cran() is working for me, don't know what changed.

fdschneider · 2020-04-05T06:23:27Z

I also have this error when running on Windows 10 rhub::check(platform = "debian-clang-devel") or rhub::check_for_cran().

Output:
https://builder.r-hub.io/status/traitdataform_0.5.7.tar.gz-8a821ff1db8548bd88f3d0b047e38ebc

Error arises when starting Docker container

 717#> ==================================================
 718#> downloaded 39 KB
 719#> * installing *source* package 'BiocManager' ...
 720#> ** package 'BiocManager' successfully unpacked and MD5 sums checked
 721#> ** using staged installation
 722#> ** R
 723#> ** inst
 724#> ** byte-compile and prepare package for lazy loading
 725#> ** help
 726#> *** installing help indices
 727#> ** building package indices
 728#> ** installing vignettes
 729#> ** testing if installed package can be loaded from temporary location
 730#> Error: package or namespace load failed for 'BiocManager':
 731#> .onAttach failed in attachNamespace() for 'BiocManager', details:
 732#> call: if (version[, 1:2] != version) return(sprintf("version '%s' must have two components, e.g., '3.7'",
 733#> error: argument is of length zero
 734#> Error: loading failed
 735#> Execution halted
 736#> ERROR: loading failed
 737#> * removing '/home/docker/R/BiocManager'
 738#> The downloaded source packages are in
 739#> '/tmp/Rtmpa093zU/downloaded_packages'
 740#> Warning message:
 741#> In install.packages("BiocManager") :
 742#> installation of package 'BiocManager' had non-zero exit status
 743#> >
 744#> >

phargarten2 mentioned this issue Dec 12, 2019

preperror #321

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CRAN Failing on r-devel-linux-x86_64-debian-clang #318

CRAN Failing on r-devel-linux-x86_64-debian-clang #318

elinw commented Nov 24, 2019

gaborcsardi commented Nov 24, 2019

elinw commented Nov 25, 2019 •

edited by gaborcsardi

gaborcsardi commented Nov 25, 2019

elinw commented Nov 26, 2019

gaborcsardi commented Nov 26, 2019

elinw commented Nov 27, 2019 •

edited

elinw commented Nov 28, 2019

HeidiSeibold commented Dec 10, 2019

phargarten2 commented Dec 12, 2019 •

edited

elinw commented Feb 2, 2020

fdschneider commented Apr 5, 2020

CRAN Failing on r-devel-linux-x86_64-debian-clang #318

CRAN Failing on r-devel-linux-x86_64-debian-clang #318

Comments

elinw commented Nov 24, 2019

gaborcsardi commented Nov 24, 2019

elinw commented Nov 25, 2019 • edited by gaborcsardi

gaborcsardi commented Nov 25, 2019

elinw commented Nov 26, 2019

gaborcsardi commented Nov 26, 2019

elinw commented Nov 27, 2019 • edited

elinw commented Nov 28, 2019

HeidiSeibold commented Dec 10, 2019

phargarten2 commented Dec 12, 2019 • edited

elinw commented Feb 2, 2020

fdschneider commented Apr 5, 2020

elinw commented Nov 25, 2019 •

edited by gaborcsardi

elinw commented Nov 27, 2019 •

edited

phargarten2 commented Dec 12, 2019 •

edited