Build fails on Linux (rplexos 1.11)

danielsjf commented 7 years ago

https://cran.r-project.org/web/checks/check_results_rplexos.html

danielsjf commented 7 years ago

@claytonpbarrows Do you know how I could contact the owner of the NREL organisation? I would like to get administrator right on this repository. Via AppVeyor, I could test the builds on linux too. Unfortunately I cannot make AppVeyor work if I don't have the administrator rights.

danielsjf commented 7 years ago

@NRELAdmin Would it be possible to grant me administrator rights on this repository? As mentioned above, I would like to try AppVeyor to test on Linux to resolve an issue. Unfortunately I can only use AppVeyor when I'm an administrator.

claytonpbarrows commented 7 years ago

@danielsjf if you can't get admin rom NREL, let me know how I can help.

claytonpbarrows commented 7 years ago

@danielsjf the build in commit 3d5499ced54049d0f57c9b93028359feb37dcb82 is successful on linux, but the unit_tests still fail:

> Sys.info()
                                      sysname                                       release 
                                      "Linux"                            "4.4.0-47-generic" 
                                      version                                      nodename 
"#68-Ubuntu SMP Wed Oct 26 19:39:52 UTC 2016"                      "monkeycup.hpc.nrel.gov" 
                                      machine                                         login 
                                     "x86_64"                                     "unknown" 
                                         user                                effective_user 
                                   "cbarrows"                                    "cbarrows"

danielsjf commented 7 years ago

@claytonpbarrows NRELAdmin doesn't seem to respond. Do you know how I could contact the admin directly via an email address?

Could you specify which unit tests fail and with which error messages? Also, I think that the linux version did build before, but the checks were not all positive. Could you post the results of devtools::check()

claytonpbarrows commented 7 years ago

> devtools::check()
Updating rplexos documentation
Loading rplexos
Setting env vars ---------------------------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building rplexos ---------------------------------------------------------------------------------
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD build  \
  '/home/cbarrows/rplexos' --no-resave-data --no-manual 

* checking for file ‘/home/cbarrows/rplexos/DESCRIPTION’ ... OK
* preparing ‘rplexos’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘rplexos/packrat’
* building ‘rplexos_1.1.12.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Setting env vars ---------------------------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_           : FALSE
_R_CHECK_FORCE_SUGGESTS_          : FALSE
Checking rplexos ---------------------------------------------------------------------------------
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD check  \
  '/tmp/RtmpOhdAm5/rplexos_1.1.12.tar.gz' --as-cran --timings --no-manual 

* using log directory ‘/tmp/RtmpOhdAm5/rplexos.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘rplexos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rplexos’ version ‘1.1.12’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/extdata/zip_bin/msys-2.0.dll
  inst/extdata/zip_bin/msys-iconv-2.dll
  inst/extdata/zip_bin/msys-intl-8.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... WARNING
Found the following executable files:
  inst/extdata/zip_bin/dd.exe
  inst/extdata/zip_bin/msys-2.0.dll
  inst/extdata/zip_bin/msys-iconv-2.dll
  inst/extdata/zip_bin/msys-intl-8.dll
  inst/extdata/zip_bin/sh.exe
  inst/extdata/zip_bin/unzip.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rplexos’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      1.8Mb
* 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
* 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 line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [16s/16s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: Expected errors and warnings (@test_process.R#49) ------------------
  process_folder(c(loc, locERR)) did not throw an error.

  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
    there is no package called 'nlme'
  Error: package or namespace load failed for 'tidyverse'
  testthat results ================================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: Expected errors and warnings (@test_process.R#49) 

  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/tmp/RtmpOhdAm5/rplexos.Rcheck/00check.log’
for details.

R CMD check results
1 error  | 1 warning  | 2 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: Expected errors and warnings (@test_process.R#49) ------------------
  process_folder(c(loc, locERR)) did not throw an error.

  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
    there is no package called 'nlme'
  Error: package or namespace load failed for 'tidyverse'
  testthat results ================================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: Expected errors and warnings (@test_process.R#49) 

  Error: testthat unit tests failed
  Execution halted

checking for executable files ... WARNING
Found the following executable files:
  inst/extdata/zip_bin/dd.exe
  inst/extdata/zip_bin/msys-2.0.dll
  inst/extdata/zip_bin/msys-iconv-2.dll
  inst/extdata/zip_bin/msys-intl-8.dll
  inst/extdata/zip_bin/sh.exe
  inst/extdata/zip_bin/unzip.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/extdata/zip_bin/msys-2.0.dll
  inst/extdata/zip_bin/msys-iconv-2.dll
  inst/extdata/zip_bin/msys-intl-8.dll
Object files/libraries should not be included in a source package.

checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      1.8Mb

danielsjf commented 7 years ago

Thanks. I'll investigate this.

claytonpbarrows commented 7 years ago

I was able to fix the package dependencies for the testing process in 8210b8d14f7edccc5f337263e521e8471030e3ec, and the previous commit solves one of the tests, but several tests still fail:

> devtools::check()
Updating rplexos documentation
Loading rplexos
Setting env vars ---------------------------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building rplexos ---------------------------------------------------------------------------------
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD build  \
  '/home/cbarrows/rplexos' --no-resave-data --no-manual 

* checking for file ‘/home/cbarrows/rplexos/DESCRIPTION’ ... OK
* preparing ‘rplexos’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘rplexos/packrat’
* building ‘rplexos_1.1.12.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Setting env vars ---------------------------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_           : FALSE
_R_CHECK_FORCE_SUGGESTS_          : FALSE
Checking rplexos ---------------------------------------------------------------------------------
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD check  \
  '/tmp/RtmpPiyIpz/rplexos_1.1.12.tar.gz' --as-cran --timings --no-manual 

* using log directory ‘/tmp/RtmpPiyIpz/rplexos.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘rplexos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rplexos’ version ‘1.1.12’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/executables/win32/zip_bin/msys-2.0.dll
  inst/executables/win32/zip_bin/msys-iconv-2.dll
  inst/executables/win32/zip_bin/msys-intl-8.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... WARNING
Found the following executable files:
  inst/executables/win32/zip_bin/dd.exe
  inst/executables/win32/zip_bin/msys-2.0.dll
  inst/executables/win32/zip_bin/msys-iconv-2.dll
  inst/executables/win32/zip_bin/msys-intl-8.dll
  inst/executables/win32/zip_bin/sh.exe
  inst/executables/win32/zip_bin/unzip.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rplexos’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    executables   4.5Mb
    libs          1.8Mb
* 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
* 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 line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [61s/73s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: expect_equal(read_zip(file_zip, file_bin_rel, raw(1), 5, 4), as.raw(1:16)[6:9]) at testthat/test_zip.R:33
  2: compare(object, expected, ...)
  3: read_zip(file_zip, file_bin_rel, raw(1), 5, 4)
  4: stop("The on-the-fly mode currently only works for Windows.")

  testthat results ================================================================
  OK: 150 SKIPPED: 1 FAILED: 3
  1. Failure: Process on the fly (@test_process.R#62) 
  2. Error: Read zip (@test_zip.R#25) 
  3. Error: Seek (@test_zip.R#33) 

  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/tmp/RtmpPiyIpz/rplexos.Rcheck/00check.log’
for details.

R CMD check results
1 error  | 1 warning  | 2 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: expect_equal(read_zip(file_zip, file_bin_rel, raw(1), 5, 4), as.raw(1:16)[6:9]) at testthat/test_zip.R:33
  2: compare(object, expected, ...)
  3: read_zip(file_zip, file_bin_rel, raw(1), 5, 4)
  4: stop("The on-the-fly mode currently only works for Windows.")

  testthat results ================================================================
  OK: 150 SKIPPED: 1 FAILED: 3
  1. Failure: Process on the fly (@test_process.R#62) 
  2. Error: Read zip (@test_zip.R#25) 
  3. Error: Seek (@test_zip.R#33) 

  Error: testthat unit tests failed
  Execution halted

checking for executable files ... WARNING
Found the following executable files:
  inst/executables/win32/zip_bin/dd.exe
  inst/executables/win32/zip_bin/msys-2.0.dll
  inst/executables/win32/zip_bin/msys-iconv-2.dll
  inst/executables/win32/zip_bin/msys-intl-8.dll
  inst/executables/win32/zip_bin/sh.exe
  inst/executables/win32/zip_bin/unzip.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/executables/win32/zip_bin/msys-2.0.dll
  inst/executables/win32/zip_bin/msys-iconv-2.dll
  inst/executables/win32/zip_bin/msys-intl-8.dll
Object files/libraries should not be included in a source package.

checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    executables   4.5Mb
    libs          1.8Mb

NREL / rplexos

Build fails on Linux (rplexos 1.11) #60