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richelbilderbeek / mhcnuggetsr

Package to call MHCnuggets from R, to predict MHC-I and MHC-II epitopes
GNU General Public License v3.0
4 stars 1 forks source link

Fix CRAN submission mhcnuggetsr 1.1 #8

Open richelbilderbeek opened 4 years ago

richelbilderbeek commented 4 years ago 
26 July 2020 12:58 9 KB
From: [ligges]
To: [richel]
Cc: [CRAN-submissions]

Dear maintainer,

package mhcnuggetsr_1.1.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200726_122621/Windows/00check.log>
Status: 2 ERRORs, 1 WARNING, 1 NOTE
Debian: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200726_122621/Debian/00check.log>
Status: 1 NOTE

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200726_122621/>
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>'

New submission

Possibly mis-spelled words in DESCRIPTION:
MHC (9:21, 9:37)
MHCnuggets (2:13, 8:5, 10:37)
epitopes (9:50)

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'i386', Result: ERROR
Running examples in 'mhcnuggetsr-Ex.R' failed
The error most likely occurred in:

    base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    ### Name: mhcnuggetsr_report
    ### Title: Create a mhcnuggetsr report, to be used when reporting bugs
    ### Aliases: mhcnuggetsr_report

    ### ** Examples

    mhcnuggetsr_report()

***************
* mhcnuggetsr *
***************
OS: win
Python available: FALSE
Warning in system2(command = python, args = paste0("\"", config_script, :
running command '"C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "D:/temp/RtmpAPdt2c/RLIBS_23f1c29f1532f/reticulate/config/config.py"' had status 2
Error in python_config(miniconda_python, NULL, miniconda_python) :
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
Calls: mhcnuggetsr_report ... initialize_python -> py_discover_config -> python_config
Execution halted

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'x64', Result: ERROR
Running examples in 'mhcnuggetsr-Ex.R' failed
The error most likely occurred in:

    base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    ### Name: mhcnuggetsr_report
    ### Title: Create a mhcnuggetsr report, to be used when reporting bugs
    ### Aliases: mhcnuggetsr_report

    ### ** Examples

    mhcnuggetsr_report()

***************
* mhcnuggetsr *
***************
OS: win
Python available: FALSE
Warning in system2(command = python, args = paste0("\"", config_script, :
running command '"C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "D:/temp/RtmpAPdt2c/RLIBS_23f1c29f1532f/reticulate/config/config.py"' had status 2
Error in python_config(miniconda_python, NULL, miniconda_python) :
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
Calls: mhcnuggetsr_report ... initialize_python -> py_discover_config -> python_config
Execution halted

Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown
Quitting from lines 161-162 (demo.Rmd)
Error: processing vignette 'demo.Rmd' failed with diagnostics:
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
--- failed re-building 'demo.Rmd'

SUMMARY: processing the following file failed:
'demo.Rmd'

Error: Vignette re-building failed.
Execution halted
richelbilderbeek commented 4 years ago 
[CRAN-pretest-archived] CRAN submission mhcnuggetsr 1.1

24 August 2020 09:45 9 KB
From: [ligges]
To: [richel]
Cc: [CRAN-submissions]

Dear maintainer,

package mhcnuggetsr_1.1.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200824_091956/Windows/00check.log>
Status: 2 ERRORs, 1 WARNING, 1 NOTE
Debian: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200824_091956/Debian/00check.log>
Status: 1 NOTE

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200824_091956/>
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>'

New submission

Possibly mis-spelled words in DESCRIPTION:
MHC (9:21, 9:37)
MHCnuggets (2:13, 8:5, 10:37)
epitopes (9:50)

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'i386', Result: ERROR
Running examples in 'mhcnuggetsr-Ex.R' failed
The error most likely occurred in:

    base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    ### Name: get_pip_version
    ### Title: Get the version of pip
    ### Aliases: get_pip_version

    ### ** Examples

    if (is_pip_installed()) {

+ get_pip_version()
+ }
Warning in system2(command = python, args = paste0("\"", config_script, :
running command '"C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "D:/temp/Rtmpe8DW7n/RLIBS_1c85018a3639/reticulate/config/config.py"' had status 2
Error in python_config(miniconda_python, NULL, miniconda_python) :
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
Calls: is_pip_installed ... initialize_python -> py_discover_config -> python_config
Execution halted

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'x64', Result: ERROR
Running examples in 'mhcnuggetsr-Ex.R' failed
The error most likely occurred in:

    base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    ### Name: get_pip_version
    ### Title: Get the version of pip
    ### Aliases: get_pip_version

    ### ** Examples

    if (is_pip_installed()) {

+ get_pip_version()
+ }
Warning in system2(command = python, args = paste0("\"", config_script, :
running command '"C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "D:/temp/Rtmpe8DW7n/RLIBS_1c85018a3639/reticulate/config/config.py"' had status 2
Error in python_config(miniconda_python, NULL, miniconda_python) :
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
Calls: is_pip_installed ... initialize_python -> py_discover_config -> python_config
Execution halted

Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown
Quitting from lines 161-162 (demo.Rmd)
Error: processing vignette 'demo.Rmd' failed with diagnostics:
Error 2 occurred running C:/Users/ligges/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
--- failed re-building 'demo.Rmd'

SUMMARY: processing the following file failed:
'demo.Rmd'

Error: Vignette re-building failed.
Execution halted
richelbilderbeek commented 4 years ago

Just discovered rhub! Just do: rhub::check() to check for a build :+1:

richelbilderbeek commented 4 years ago

New results from submission:


[CRAN-pretest-archived] CRAN submission mhcnuggetsr 1.1

26 August 2020 10:35 7 KB
From: [ligges]
To: [richel]
Cc: [CRAN-submissions]

Dear maintainer,

package mhcnuggetsr_1.1.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200825_140950/Windows/00check.log>
Status: 2 NOTEs
Debian: <https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200825_140950/Debian/00check.log>
Status: 1 NOTE

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/mhcnuggetsr_1.1_20200825_140950/>
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>'

New submission

Possibly mis-spelled words in DESCRIPTION:
MHC (9:21, 9:37)
MHCnuggets (2:13, 8:5, 10:37)
epitopes (9:50)

Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'i386', Result: NOTE
Examples with CPU (user + system) or elapsed time > 10s
user system elapsed
mhcnuggetsr_report 0.09 0.13 10.28