forked from rdiaz02/OncoSimul
-
Notifications
You must be signed in to change notification settings - Fork 0
/
put-in-bioc-dir-and-test.sh-former-subversion
executable file
·126 lines (103 loc) · 5.29 KB
/
put-in-bioc-dir-and-test.sh-former-subversion
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
#!/bin/bash
## This places the code to upload to BiC in the right place.
## The Subversion-in-BioC directory is a special directory (under svn vc)
## for the code in BioC. Yes, will eventually use
## the bridge or similar.
## If passed an additional argument, with the path of an R version, it
## builds and tests.
## Yes, works under eshell.
## I need to clean up first, because otherwise when I remove files in the
## master git repo, they are not necessarily removed in the svn repo
rm ./Subversion-in-BioC/OncoSimulR/vignettes/*
rm ./Subversion-in-BioC/OncoSimulR/tests/*
rm ./Subversion-in-BioC/OncoSimulR/tests/manual/*
rm ./Subversion-in-BioC/OncoSimulR/tests/testthat/*
rm ./Subversion-in-BioC/OncoSimulR/src/*
rm ./Subversion-in-BioC/OncoSimulR/R/*
rm ./Subversion-in-BioC/OncoSimulR/man/*
rm ./Subversion-in-BioC/OncoSimulR/inst/*
rm ./Subversion-in-BioC/OncoSimulR/data/*
rm ./Subversion-in-BioC/OncoSimulR/inst/miscell/*
cp OncoSimulR/vignettes/relfunct.tex ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/preamble.tex ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/relfunct.png ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/custom4.css ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/OncoSimulR.Rmd ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/OncoSimulR.bib ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitsetinfo.sty ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitinfo.sty ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitHeadInfo.gin ./Subversion-in-BioC/OncoSimulR/vignettes/.
cp OncoSimulR/src/*.c ./Subversion-in-BioC/OncoSimulR/src/.
cp OncoSimulR/src/*.cpp ./Subversion-in-BioC/OncoSimulR/src/.
cp OncoSimulR/src/*.h ./Subversion-in-BioC/OncoSimulR/src/.
cp OncoSimulR/src/Makevars* ./Subversion-in-BioC/OncoSimulR/src/.
cp OncoSimulR/R/*.R ./Subversion-in-BioC/OncoSimulR/R/.
cp OncoSimulR/tests/testthat.R ./Subversion-in-BioC/OncoSimulR/tests/.
cp OncoSimulR/tests/testthat/*.R ./Subversion-in-BioC/OncoSimulR/tests/testthat/.
cp OncoSimulR/tests/manual/*.R ./Subversion-in-BioC/OncoSimulR/tests/manual/.
cp OncoSimulR/tests/manual/*.txt ./Subversion-in-BioC/OncoSimulR/tests/manual/.
cp OncoSimulR/tests/*.txt ./Subversion-in-BioC/OncoSimulR/tests/.
cp OncoSimulR/man/*.Rd ./Subversion-in-BioC/OncoSimulR/man/.
cp OncoSimulR/inst/NEWS ./Subversion-in-BioC/OncoSimulR/inst/.
cp OncoSimulR/inst/CITATION ./Subversion-in-BioC/OncoSimulR/inst/.
cp OncoSimulR/inst/miscell/example-binom-problems.cpp ./Subversion-in-BioC/OncoSimulR/inst/miscell/.
cp OncoSimulR/inst/miscell/*.R ./Subversion-in-BioC/OncoSimulR/inst/miscell/.
cp OncoSimulR/data/*.RData ./Subversion-in-BioC/OncoSimulR/data/.
cp OncoSimulR/NAMESPACE ./Subversion-in-BioC/OncoSimulR/.
cp OncoSimulR/DESCRIPTION ./Subversion-in-BioC/OncoSimulR/.
## should we run the tests?
if [[ $# == 1 ]]; then
V_R=$1
cd ~/Proyectos/OncoSimul/Subversion-in-BioC
V_P=$(cat ./OncoSimulR/DESCRIPTION | grep Version | cut -d' ' -f2)
rm OncoSimulR_$V_P.tar.gz
## As shown in build report from BioC
# echo " ***************************************** "
# echo " ********* R CMD build ************** "
# echo " "
# time $V_R CMD build --keep-empty-dirs --no-resave-data OncoSimulR
# echo " "
# echo " =========== done R CMD build ========== "
# echo " "
# ## As shown in check report from BioC
# echo " *************************************************** "
# echo " **** R CMD check , as in check report **** "
# echo ""
# time $V_R CMD check --no-vignettes --timings OncoSimulR_$V_P.tar.gz
# echo " "
# echo " ========= done R CMD check as in check report ======= "
# echo " "
## time as explained in https://www.bioconductor.org/developers/package-guidelines/#correctness
# echo " ************************************ "
# echo " ***** R CMD check: time OK? ***** "
# echo ""
# time $V_R CMD check --no-build-vignettes OncoSimulR_$V_P.tar.gz
# echo " "
# echo " =========== done R CMD check time OK? ========== "
## As shown in build report from BioC
echo " ***************************************** "
echo " ********* R CMD build vanilla ************** "
echo " "
time $V_R --vanilla CMD build --keep-empty-dirs --no-resave-data OncoSimulR
echo " "
echo " =========== done R CMD build vanilla ========== "
echo " "
## As shown in check report from BioC
echo " *************************************************** "
echo " **** R CMD check vanilla , as in check report **** "
echo ""
time $V_R --vanilla CMD check --no-vignettes --timings OncoSimulR_$V_P.tar.gz
echo " "
echo " ========= done R CMD check vanilla as in check report ======= "
echo " "
## time as explained in https://www.bioconductor.org/developers/package-guidelines/#correctness
echo " ************************************ "
# echo " ***** R CMD check: time OK? ***** "
# echo ""
# time $V_R --vanilla CMD check --no-build-vignettes OncoSimulR_$V_P.tar.gz
# echo " "
# echo " =========== done R CMD check vanilla time OK? ========== "
fi
## Check what/if things need adding
cd ~/Proyectos/OncoSimul/Subversion-in-BioC/OncoSimulR
svn status --show-updates