Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

linux builds consistently have `PREPERROR` #173

Open
IndrajeetPatil opened this issue Nov 17, 2018 · 4 comments

Comments

Projects
None yet
2 participants
@IndrajeetPatil
Copy link

commented Nov 17, 2018

When I test linux builds for my package on r-hub, they consistently tend to have PREPERROR due to failure to download dependencies. But I never have such issues either with Travis or AppVeyor.

  • Ubuntu Linux 16.04 LTS, R-release, GCC
Running `R CMD build`...
* checking for file/tmp/RtmpQ3NxiK/remotes1051016ec2/ggstatsplot/DESCRIPTION... OK
* preparingggstatsplot:
* checking DESCRIPTION meta-information ... OK
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if adata/datalistfile should be added
* buildingggstatsplot_0.0.6.9000.tar.gzInstalling package into/home/docker/R’
(aslibis unspecified)
ERROR: this R is version 3.4.4, package 'ggstatsplot' requires R >=  3.5.0
Warning messages:
1: In i.p(...) :
  installation of packageordinalhad non-zero exit status
2: In i.p(...) :
  installation of packagegroupedstatshad non-zero exit status
3: In i.p(...) :
  installation of package/tmp/RtmpQ3NxiK/file1055bacf0aa/ggstatsplot_0.0.6.9000.tar.gzhad non-zero exit status
> 
> 
> library(ggstatsplot)
Error in library(ggstatsplot) : there is no package calledggstatsplotExecution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/ggstatsplot_0.0.6.9000.tar.gz-69c7048910914a71a37a7124790d93bc/2018-11-17T20:49:23Z
{"status":"ok"}
Finished: FAILURE
  • Platform: CentOS 6, stock R from EPEL
Running `R CMD build`...
* checking for file/tmp/RtmpIccCHK/remotesf02f2c688e/ggstatsplot/DESCRIPTION... OK
* preparingggstatsplot:
* checking DESCRIPTION meta-information ... OK
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if adata/datalistfile should be added
* buildingggstatsplot_0.0.6.9000.tar.gzInstalling package into/home/docker/R’
(aslibis unspecified)
ERROR: dependencypaletteeris not available for packageggstatsplot* removing/home/docker/R/ggstatsplotWarning messages:
1: In i.p(...) : installation of packagerglhad non-zero exit status
2: In i.p(...) : installation of packagepalshad non-zero exit status
3: In i.p(...) :
  installation of packagepaletteerhad non-zero exit status
4: In i.p(...) :
  installation of package/tmp/RtmpIccCHK/filef010b954c6/ggstatsplot_0.0.6.9000.tar.gzhad non-zero exit status
> 
> 
> library(ggstatsplot)
Error in library(ggstatsplot) : there is no package calledggstatsplotExecution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/ggstatsplot_0.0.6.9000.tar.gz-d62badfeeb5443d497639c5b072b5672/2018-11-17T16:07:23Z
{"status":"ok"}
Finished: FAILURE
  • Platform: Fedora Linux, R-devel, GCC
Running `R CMD build`...
* checking for file/tmp/RtmpcH0Oe3/remotesfa13374c08/ggstatsplot/DESCRIPTION... OK
* preparingggstatsplot:
* checking DESCRIPTION meta-information ... OK
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if adata/datalistfile should be added
* buildingggstatsplot_0.0.6.9000.tar.gzInstalling package into/home/docker/R’
(aslibis unspecified)
ERROR: dependencypaletteeris not available for packageggstatsplot* removing/home/docker/R/ggstatsplotWarning messages:
1: In i.p(...) : installation of packagerglhad non-zero exit status
2: In i.p(...) : installation of packagepalshad non-zero exit status
3: In i.p(...) :
  installation of packagepaletteerhad non-zero exit status
4: In i.p(...) :
  installation of package/tmp/RtmpcH0Oe3/filefa1f08b4d/ggstatsplot_0.0.6.9000.tar.gzhad non-zero exit status
> 
> 
> library(ggstatsplot)
Error in library(ggstatsplot) : there is no package calledggstatsplotExecution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/ggstatsplot_0.0.6.9000.tar.gz-81849ada29bb48d09518a37fbb55c35a/2018-11-17T19:02:23Z
{"status":"ok"}
Finished: FAILURE
  • Platform: Debian Linux, R-release, GCC
Running `R CMD build`...
* checking for file/tmp/RtmpMy8a6r/remotesf3badbbe4/ggstatsplot/DESCRIPTION... OK
* preparingggstatsplot:
* checking DESCRIPTION meta-information ... OK
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if adata/datalistfile should be added
* buildingggstatsplot_0.0.6.9000.tar.gzInstalling package into/home/docker/R’
(aslibis unspecified)
ERROR: dependencypaletteeris not available for packageggstatsplot* removing/home/docker/R/ggstatsplotWarning messages:
1: In i.p(...) : installation of packagerglhad non-zero exit status
2: In i.p(...) :> 
> 
 installation of packagepalshad non-zero exit status
3: In i.p(...) :
  installation of packagepaletteerhad non-zero exit status
4: In i.p(...) :
  installation of package/tmp/RtmpMy8a6r/filef31f4502e/ggstatsplot_0.0.6.9000.tar.gzhad non-zero exit status
> library(ggstatsplot)
Error in library(ggstatsplot) : there is no package calledggstatsplotExecution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/ggstatsplot_0.0.6.9000.tar.gz-2a2b7013328f4239a6e42b34946e0740/2018-11-17T19:55:27Z
{"status":"ok"}
Finished: FAILURE

Etc.

#--------------------------------------------------------------------------------------

The only exception to this is MacOS

  • macOS 10.11 El Capitan, R-release (experimental)
>>>>>============== Running R CMD check
* using log directory/Users/userlNlJ5hbg/ggstatsplot.Rcheck* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for fileggstatsplot/DESCRIPTION... OK
* checking extension type ... Package
* this is packageggstatsplotversion0.0.6.9000* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether packageggstatsplotcan be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   3.4Mb
* checking package directory ... OK
* checkingbuilddirectory ... 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
* 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 ... 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 contents ofdatadirectory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files frominst/doc... OK
* checking files invignettes... OK
* checking examples ... OK
* checking for unstated dependencies intests... OK
* checking tests ...
  Runningspelling.RRunningtestthat.ROK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ininst/doc... OK
* checking running R code from vignettes ...additional.RmdusingUTF-8... OKggbetweenstats.RmdusingUTF-8... OKggcoefstats.RmdusingUTF-8... OKggcorrmat.RmdusingUTF-8... OKgghistostats.RmdusingUTF-8... OKggpiestats.RmdusingUTF-8... OKggscatterstats.RmdusingUTF-8... OKtests_and_coverage.RmdusingUTF-8... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See/Users/userlNlJ5hbg/ggstatsplot.Rcheck/00check.logfor details.


>>>>>============== Done with R CMD check
Cleaning up Xvfb
No matching processes belonging to you were found
Saving artifacts
Cleaning up user and home directory
SSH: Connecting from host [Rhubs-Mac-3.local]
SSH: Connecting with configuration [files] ...
SSH: Disconnecting configuration [files] ...
SSH: Transferred 7 file(s)
Build step 'Send files or execute commands over SSH' changed build result to SUCCESS
Pinging https://builder.r-hub.io/build/SUCCESS/ggstatsplot_0.0.6.9000.tar.gz-196f53e2a94f40efb62a2221e7fb4e4f/2018-11-17T20:09:46Z
{"status":"ok"}
Finished: SUCCESS
@gaborcsardi

This comment has been minimized.

Copy link
Member

commented Nov 17, 2018

I am not sure why that is, R-hub should install the proper packages for rgl: https://sysreqs.r-hub.io/pkg/rgl

I'll take a look.

@gaborcsardi

This comment has been minimized.

Copy link
Member

commented Nov 17, 2018

Yes, this looks like a bug in the system requirements server. Will fix very soon.

@IndrajeetPatil

This comment has been minimized.

Copy link
Author

commented Nov 22, 2018

Even when the builds do succeed, there is surprisingly still a PREPERROR warning

rhub

@IndrajeetPatil

This comment has been minimized.

Copy link
Author

commented Dec 20, 2018

Here is an even more thorough check on this issue. I restricted myself only to release, patched, and devel versions of R and checked package builds on all available platforms:

# creating a dataframe of all platforms
rhub_platforms <- tibble::as_tibble(rhub::platforms()) %>%
  dplyr::filter(.data = ., rversion != "r-oldrel")

# simultaneously triggering build on all platforms
purrr::pmap(
  .l = list(
    platform = list(rhub_platforms$name),
    email = list("redacted@gmail.com")
  ),
  .f = rhub::check
)

The submitted build succeeds both on Appveyor and Travis.
But, on rhub, out of 20 platforms, it succeeds only on 3 platforms- all Windows.

image

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.