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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

Export install_mhcnuggets and uninstall_mhcnuggets again #2

Closed richelbilderbeek closed 4 years ago

richelbilderbeek commented 4 years ago

Describe the bug

(un)?install_mhcnuggets is not exported anymore, since this commit.

To Reproduce

Actually, also that build now fails:

git clone https://github.com/richelbilderbeek/mhcnuggetsr
cd mhcnuggetsr 
#git checkout 207e49cb4c396a8f6bd03e7ed0d0771d4c87a0b0

git checkout e9e136e2a6a592fce9f104cab753539247bb83fb
echo "**************************************************"
echo "With 'install_mhcnuggets' exported:"
echo "**************************************************"
cat NAMESPACE
Rscript -e 'devtools::document()'
echo "**************************************************"
echo "Unexpected: Without 'install_mhcnuggets' exported:"
echo "**************************************************"
cat NAMESPACE
echo "**************************************************"
echo "Diff:"
echo "**************************************************"
git --no-pager diff

This will remove the install_ and uninstall_ lines:

M   NAMESPACE
D   man/install_mhcnuggets.Rd
D   man/uninstall_mhcnuggets.Rd
**************************************************
With 'install_mhcnuggets' exported:
**************************************************
# Generated by roxygen2: do not edit by hand

export(check_mhcnuggets_installation)
export(epitope_predict)
export(get_default_mhcnuggets_folder)
export(get_example_filename)
export(get_example_filenames)
export(get_mhc_1_haplotypes)
export(get_mhc_2_haplotypes)
export(get_mhcnuggets_url)
export(get_mhcnuggets_version)
export(get_pip_version)
export(get_trained_mhc_1_haplotypes)
export(get_trained_mhc_2_haplotypes)
export(is_mhcnuggets_installed)
export(is_on_appveyor)
export(is_on_ci)
export(is_on_travis)
export(mhcnuggetsr_report)
Writing NAMESPACE
Writing NAMESPACE
**************************************************
Unexpected: Without 'install_mhcnuggets' exported:
**************************************************
# Generated by roxygen2: do not edit by hand

export(check_mhcnuggets_installation)
export(epitope_predict)
export(get_default_mhcnuggets_folder)
export(get_example_filename)
export(get_example_filenames)
export(get_mhc_1_haplotypes)
export(get_mhc_2_haplotypes)
export(get_mhcnuggets_url)
export(get_mhcnuggets_version)
export(get_pip_version)
export(get_trained_mhc_1_haplotypes)
export(get_trained_mhc_2_haplotypes)
export(is_mhcnuggets_installed)
export(is_on_appveyor)
export(is_on_ci)
export(is_on_travis)
export(mhcnuggetsr_report)
**************************************************
Diff:
**************************************************
diff --git a/NAMESPACE b/NAMESPACE
index 9a041ea..66ae239 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,10 +12,8 @@ export(get_mhcnuggets_version)
 export(get_pip_version)
 export(get_trained_mhc_1_haplotypes)
 export(get_trained_mhc_2_haplotypes)
-export(install_mhcnuggets)
 export(is_mhcnuggets_installed)
 export(is_on_appveyor)
 export(is_on_ci)
 export(is_on_travis)
 export(mhcnuggetsr_report)
-export(uninstall_mhcnuggets)
diff --git a/man/install_mhcnuggets.Rd b/man/install_mhcnuggets.Rd
deleted file mode 100644
index 7b038e2..0000000
--- a/man/install_mhcnuggets.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/install_mhcnuggets.R
-\name{install_mhcnuggets}
-\alias{install_mhcnuggets}
-\title{Install the MHCnuggets Python package.}
-\usage{
-install_mhcnuggets(
-  folder_name = get_default_mhcnuggets_folder(),
-  mhcnuggets_url = get_mhcnuggets_url()
-)
-}
-\arguments{
-\item{folder_name}{superfolder of MHCnuggets.
-The superfolder's name is \code{/home/[user_name]/.local/share}
-by default, as can be obtained by
-\link{get_default_mhcnuggets_folder}}
-
-\item{mhcnuggets_url}{URL to the MHCnuggets GitHub repository}
-}
-\description{
-Install the MHCnuggets Python package.
-}
-\examples{
-library(testthat)
-
-if (1 == 2 && is_on_ci() && !is_mhcnuggets_installed()) {
-  install_mhcnuggets()
-  expect_true(is_mhcnuggets_installed())
-}
-}
-\author{
-Richèl J.C. Bilderbeek
-}
diff --git a/man/uninstall_mhcnuggets.Rd b/man/uninstall_mhcnuggets.Rd
deleted file mode 100644
index c108d77..0000000
--- a/man/uninstall_mhcnuggets.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/uninstall_mhcnuggets.R
-\name{uninstall_mhcnuggets}
-\alias{uninstall_mhcnuggets}
-\title{Uninstall the MHCnuggets Python package.}
-\usage{
-uninstall_mhcnuggets(
-  folder_name = get_default_mhcnuggets_folder(),
-  mhcnuggets_url = get_mhcnuggets_url()
-)
-}
-\arguments{
-\item{folder_name}{superfolder of MHCnuggets.
-The superfolder's name is \code{/home/[user_name]/.local/share}
-by default, as can be obtained by
-\link{get_default_mhcnuggets_folder}}
-
-\item{mhcnuggets_url}{URL to the MHCnuggets GitHub repository}
-}
-\description{
-Uninstall the MHCnuggets Python package.
-}
-\author{
-Richèl J.C. Bilderbeek
-}

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots to help explain your problem.

Environment: Show the results of running the following script:

***************
* mhcnuggetsr *
***************
OS: unix
Python available: FALSE
Python location: /home/richel/.local/share/r-miniconda/envs/r-reticulate/bin/python
python:         /home/richel/.local/share/r-miniconda/envs/r-reticulate/bin/python
libpython:      /home/richel/.local/share/r-miniconda/envs/r-reticulate/lib/libpython3.6m.so
pythonhome:     /home/richel/.local/share/r-miniconda/envs/r-reticulate:/home/richel/.local/share/r-miniconda/envs/r-reticulate
version:        3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)  [GCC 7.3.0]
numpy:          /home/richel/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/numpy
numpy_version:  1.18.1
pip version: 20.1.1
**************
* MHCnuggets *
**************
Is MHCnuggets installed: TRUE
MHCnuggets version: 2.3.2
***************
* sessionInfo *
***************
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /home/richel/.local/share/r-miniconda/envs/r-reticulate/lib/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6    lattice_0.20-40 crayon_1.3.4    rappdirs_0.3.1 
 [5] grid_3.6.3      lifecycle_0.2.0 jsonlite_1.6.1  magrittr_1.5   
 [9] highr_0.8       pillar_1.4.4    rlang_0.4.6     stringi_1.4.6  
[13] Matrix_1.2-18   vctrs_0.3.0     reticulate_1.16 ellipsis_0.3.1 
[17] mhcnuggetsr_0.5 tools_3.6.3     stringr_1.4.0   xfun_0.14      
[21] compiler_3.6.3  pkgconfig_2.0.3 knitr_1.28      tibble_3.0.1

Additional context Add any other context about the problem here.

richelbilderbeek commented 4 years ago

Bad was om my side: in `.Rbuildignore' I ignored 'install_mhcnuggets.R'. Thanks to Gabor for spotting this!