Skip to content

Commit 934a427

Browse files
author
d.tenenbaum
committed
don't modify url if it contains a #
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/bioC/admin/build/BBS@104161 bc3139a8-67e5-0310-9ffc-ced21a209358
0 parents  commit 934a427

File tree

1,884 files changed

+56122
-0
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

1,884 files changed

+56122
-0
lines changed

‎.gitignore

+1
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
*.pyc

‎1.9/bioc/README.TXT

+114
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,114 @@
1+
"1.9/bioc" BUILDS
2+
=================
3+
4+
5+
This is the top directory containing the set of scripts used to run
6+
the "1.9/bioc" builds. These scripts allow to run a complete BioC 1.9
7+
build (i.e. build + check of all the software packages in Bioconductor 1.9)
8+
on the following nodes:
9+
10+
Hostname OS Arch (*)
11+
-------- ------------------- --------
12+
lamb1 Linux (SUSE 10.1) x86_64
13+
wellington Linux (SUSE 9.2) i686
14+
churchill Solaris 2.9 sparc
15+
lemming Windows Server 2003 x86_64
16+
17+
(*) as reported by 'uname -p' (not 'arch'), except on Windows
18+
19+
Follow the instructions below to setup the "1.9/bioc" builds with 1 run per day.
20+
21+
NOTES:
22+
23+
- You need to have at least 4GB of free space on the BBS_WORK_TOPDIR dir
24+
partition (refer to the config.sh or config.bat files in each node subdir
25+
for the value of BBS_WORK_TOPDIR and other node specific variables).
26+
27+
- On each node, don't forget to create the 'log' and 'NodeInfo' subdirs under
28+
the BBS_WORK_TOPDIR dir! Also, make sure that the 'NodeInfo' subdir has
29+
mode 755 (having 744 is not enough to have it readable by anybody
30+
when it's going to be pushed to a Linux/Unix system).
31+
32+
- On the Windows nodes, in addition to the 'log' and 'NodeInfo' mentioned
33+
above, don't forget to create the 'tmp' and 'tmpdir' subdirs under the
34+
BBS_WORK_TOPDIR dir!
35+
36+
- On the Windows nodes, make sure that the user BBS is running as has
37+
MAKE=make defined in its environment (this allows packages that have
38+
an inst/doc/Makefile to have their vignette to build properly).
39+
40+
- On the Unix nodes, the bash --login option used in the crontabs below
41+
ensures that "run.sh" will "see" eactly the same environment than if
42+
started by hand.
43+
44+
45+
On lamb1 (main node)
46+
--------------------
47+
48+
IMPORTANT: On all other nodes, the "run.sh" job must
49+
start AFTER the "stage1.sh" job has finished on the main node,
50+
and finish BEFORE the "postrun.sh" job is started on the main node.
51+
52+
Put the following lines in the 'biocbuild' crontab:
53+
54+
# "1.9/bioc" builds (daily)
55+
01 12 * * * cd /home/biocbuild/BBS/1.9/bioc/lamb1 && ./stage1.sh >>/home/biocbuild/bbs-1.9/log/lamb1.log 2>&1
56+
55 12 * * * /bin/bash --login -c 'cd /home/biocbuild/BBS/1.9/bioc/lamb1 && ./run.sh >>/home/biocbuild/bbs-1.9/log/lamb1.log 2>&1'
57+
# IMPORTANT: Make sure this is started AFTER 'biocbuild' has finished its "run.sh" job on ALL other nodes!
58+
51 21 * * * cd /home/biocbuild/BBS/1.9/bioc/lamb1 && ./postrun.sh >>/home/biocbuild/bbs-1.9/log/lamb1.log 2>&1
59+
60+
If you want to automatically update the http://bioconductor.org/packages/1.9/bioc
61+
repo with the packages produced by the last "1.9/bioc" builds, then add the following
62+
line in the 'biocadmin' crontab (note that this is not part of the Build System,
63+
see the scripts in biocadmin@lamb1:bin for more information):
64+
65+
# Update http://bioconductor.org/packages/1.9/bioc repo with packages produced by last "1.9/bioc" builds
66+
# IMPORTANT: Make sure this is started AFTER 'biocbuild' has finished its "postrun.sh" job!
67+
41 00 * * * cd /home/biocadmin/bin && (./updateReposPkgs-1.9-bioc.sh && ./prepareRepos-1.9-bioc.sh && ./pushRepos-1.9-bioc.sh) >>/home/biocadmin/cron.log/updateRepos-1.9-bioc.log 2>&1
68+
69+
70+
On wellington
71+
-------------
72+
73+
Put the following line in the 'biocbuild' crontab:
74+
75+
# "1.9/bioc" builds (daily)
76+
53 12 * * * /bin/bash --login -c 'cd /home/biocbuild/BBS/1.9/bioc/wellington && ./run.sh >>/loc/biocbuild/bbs-1.9/log/wellington.log 2>&1'
77+
78+
79+
On churchill
80+
------------
81+
82+
Put the following line in the 'biocbuild' crontab:
83+
84+
# "1.9/bioc" builds (daily)
85+
51 12 * * * /bin/bash --login -c 'cd /home/biocbuild/BBS/1.9/bioc/churchill && ./run.sh >>/loc/biocbuild/bbs-1.9/log/churchill.log 2>&1'
86+
87+
88+
On lemming
89+
----------
90+
91+
Put the following command in the Task Scheduler:
92+
93+
D:\biocbld\BBS\1.9\bioc\lemming\run.bat >>D:\biocbld\bbs-1.9\log\lemming.log 2>&1
94+
95+
This MUST be started in:
96+
97+
D:\biocbld\BBS\1.9\bioc\lemming
98+
99+
by the 'LEMMING\biocbuild' user ("Run as:" field).
100+
101+
Other settings:
102+
- Schedule Task: Daily
103+
- Start time: 12:50 PM
104+
- Stop the task if it runs for 20 hours
105+
106+
IMPORTANT:
107+
- There is an issue with batch jobs on Windows Server 2003: if you want
108+
the batch job to be started even when the 'biocbuild' user is not logged on,
109+
then have a look at
110+
http://support.microsoft.com/?kbid=867466
111+
for how to achieve this.
112+
(Many thanks to Joe Aprile from PHS Helpdesk for the link, Joe can also
113+
help with fixing this pb.)
114+

‎1.9/bioc/STAGE2.R

+31
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
1+
### Repo where to find the no-vignettes target packages
2+
target_repo <- 'http://lamb1/BBS/1.9/bioc'
3+
4+
### Repos where to look for the dependencies of the target packages
5+
dep_repos <- c('http://bioconductor.org/packages/1.9/data/annotation',
6+
'http://bioconductor.org/packages/1.9/data/experiment',
7+
'http://bioconductor.org/packages/1.9/omegahat',
8+
'http://cran.fhcrc.org')
9+
10+
11+
updateInstalledPkgs <- function()
12+
{
13+
update.packages(repos=dep_repos, ask=FALSE)
14+
}
15+
16+
### Used for bootstrapping on Windows and Mac OS X where a few packages from
17+
### CRAN and Omegahat won't get installed by installPkgDeps() below (because
18+
### installPkgDeps installs from source)
19+
preinstallPkgs <- function()
20+
{
21+
pkgs <- c("XML", "RGtk2", "RCurl", "SSOAP", "RGtk")
22+
install.packages(pkgs, repos=dep_repos, dependencies=TRUE)
23+
}
24+
25+
installPkgDeps <- function(pkgs)
26+
{
27+
lock_dir <- file.path(.libPaths()[1], "00LOCK")
28+
unlink(lock_dir, recursive=TRUE)
29+
install.packages(pkgs, repos=c(target_repo, dep_repos), dependencies=TRUE, type='source')
30+
}
31+

‎1.9/bioc/STATS/Extract-build-times-HOWTO.TXT

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
Assuming that gopher5-20060916.log contains logs for the 2006-09-16 builds _only_
2+
3+
grep 'R CMD build ' gopher5-20060916.log | grep seconds |\
4+
sed -r "s/^.*R CMD build ([^[:space:]]+)'.* ([^[:space:]]+) seconds.*$/\2\t\1/" |\
5+
sort -nr > gopher5-20060916-build-times.txt

‎1.9/bioc/STATS/Extract-check-times-HOWTO.TXT

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
Assuming that gopher5-20060916.log contains logs for the 2006-09-16 builds _only_
2+
3+
grep check gopher5-20060916.log | grep seconds |\
4+
sed -r 's/^.* ([^[:space:]]+\.tar\.gz).* ([^[:space:]]+) seconds.*$/\2\t\1/' |\
5+
sort -nr > gopher5-20060916-check-times.txt

‎1.9/bioc/STATS/STATS.TXT

+19
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
BioC 1.9
2+
3+
BioC | pkgs in | R | gopher5 | wellington | churchill | lemming |
4+
svn | manifest | svn | | | | |
5+
date rev. | file | rev. | BUILD | CHECK | BUILD | CHECK | BUILD | CHECK | BUILD | CHECK | BUILD BIN |
6+
7+
No stats for the "install no-vig pkgs from pre-repos" stage (STAGE2).
8+
9+
A complete run took:
10+
date: Nov 22 Mar 28
11+
2005 2006
12+
stages 3,4 parallelized: no yes
13+
14+
on gopher5 (stages 2,3,4): 5h19 3h41
15+
on wellington (stages 2,3,4): 7h41 3h43
16+
on churchill (stages 2,3,4): 16h52 6h47
17+
on lemming (stages 2,3,4,5): 7h21 7h04
18+
on walpole (stages 2,3,4,5): 7h06 NA
19+
on gladstone (stages 2,3,4): NA 1h58

‎1.9/bioc/STATS/gopher5-20060813-check-times.txt

+185
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,185 @@
1+
1608.98 stam_1.5.0.tar.gz
2+
1208.32 ontoTools_1.9.0.tar.gz
3+
1112.67 GOstats_1.7.3.tar.gz
4+
1032.16 affyPLM_1.9.11.tar.gz
5+
980.22 cellHTS_1.3.26.tar.gz
6+
952.25 rflowcyt_1.5.5.tar.gz
7+
916.20 goCluster_1.7.0.tar.gz
8+
803.24 y2hStat_1.3.4.tar.gz
9+
754.09 altcdfenvs_1.7.0.tar.gz
10+
753.24 matchprobes_1.5.0.tar.gz
11+
745.32 vsn_1.11.2.tar.gz
12+
711.59 GlobalAncova_2.3.0.tar.gz
13+
681.58 pdmclass_1.5.0.tar.gz
14+
655.59 twilight_1.9.2.tar.gz
15+
632.30 ScISI_1.3.0.tar.gz
16+
586.85 sagenhaft_1.5.0.tar.gz
17+
558.03 affypdnn_1.7.0.tar.gz
18+
550.21 safe_1.5.0.tar.gz
19+
540.08 macat_1.7.2.tar.gz
20+
515.76 simulatorAPMS_1.5.0.tar.gz
21+
455.62 xcms_1.5.1.tar.gz
22+
448.90 nnNorm_1.9.0.tar.gz
23+
434.10 stepNorm_1.5.0.tar.gz
24+
413.28 affycoretools_1.5.5.tar.gz
25+
401.75 annaffy_1.5.2.tar.gz
26+
390.28 aCGH_1.7.0.tar.gz
27+
387.83 snapCGH_1.1.5.tar.gz
28+
381.22 gcrma_2.5.1.tar.gz
29+
379.83 beadarray_1.1.4.tar.gz
30+
376.13 marray_1.11.0.tar.gz
31+
344.83 affy_1.11.6.tar.gz
32+
344.72 OCplus_1.7.0.tar.gz
33+
338.79 copa_1.1.2.tar.gz
34+
330.33 MergeMaid_2.5.0.tar.gz
35+
325.74 plgem_1.5.0.tar.gz
36+
318.34 MiPP_1.5.0.tar.gz
37+
315.04 goTools_1.5.0.tar.gz
38+
304.80 DEDS_1.5.0.tar.gz
39+
302.17 pcot2_1.0.0.tar.gz
40+
287.20 adSplit_1.3.0.tar.gz
41+
282.38 annotate_1.11.4.tar.gz
42+
262.28 limma_2.7.8.tar.gz
43+
253.97 EBarrays_1.5.0.tar.gz
44+
253.13 hexbin_1.7.1.tar.gz
45+
250.63 hopach_1.7.0.tar.gz
46+
244.25 OLIN_1.9.0.tar.gz
47+
242.79 GeneMeta_1.5.0.tar.gz
48+
239.60 biomaRt_1.7.6.tar.gz
49+
236.26 LMGene_1.1.0.tar.gz
50+
228.65 PROcess_1.9.2.tar.gz
51+
227.92 edd_1.11.1.tar.gz
52+
227.90 timecourse_1.5.0.tar.gz
53+
220.81 Category_1.5.1.tar.gz
54+
218.55 makecdfenv_1.11.0.tar.gz
55+
216.54 OrderedList_1.5.2.tar.gz
56+
214.65 affyQCReport_1.11.1.tar.gz
57+
212.52 Rgraphviz_1.11.9.tar.gz
58+
206.21 MCRestimate_1.7.0.tar.gz
59+
206.14 bim_1.5.0.tar.gz
60+
192.09 RankProd_2.5.0.tar.gz
61+
180.86 BeadExplorer_1.0.0.tar.gz
62+
175.51 affydata_1.9.0.tar.gz
63+
173.61 reb_1.5.0.tar.gz
64+
170.66 genefilter_1.11.8.tar.gz
65+
167.14 ecolitk_1.5.0.tar.gz
66+
161.83 applera_1.3.0.tar.gz
67+
156.05 BioMVCClass_1.0.5.tar.gz
68+
155.39 rfcdmin_1.5.1.tar.gz
69+
155.15 aroma.light_1.1.0.tar.gz
70+
154.47 MantelCorr_1.3.0.tar.gz
71+
153.87 geneplotter_1.11.7.tar.gz
72+
153.63 prada_1.9.8.tar.gz
73+
153.40 affxparser_1.5.3.tar.gz
74+
152.88 MLInterfaces_1.5.2.tar.gz
75+
150.27 tilingArray_1.11.8.tar.gz
76+
146.09 EBImage_1.3.102.tar.gz
77+
145.26 SAGElyzer_1.11.0.tar.gz
78+
142.14 GraphAT_1.5.0.tar.gz
79+
141.01 panp_1.3.0.tar.gz
80+
140.88 AnnBuilder_1.11.6.tar.gz
81+
140.08 Biobase_1.11.26.tar.gz
82+
139.39 affycomp_1.9.0.tar.gz
83+
138.82 Resourcerer_1.7.0.tar.gz
84+
137.09 maSigPro_1.5.0.tar.gz
85+
136.85 gpls_1.5.0.tar.gz
86+
135.87 graph_1.11.12.tar.gz
87+
135.58 multtest_1.11.2.tar.gz
88+
132.04 arrayQuality_1.9.0.tar.gz
89+
131.99 pathRender_1.1.0.tar.gz
90+
130.08 mmgmos_1.5.0.tar.gz
91+
124.89 DNAcopy_1.7.0.tar.gz
92+
122.13 factDesign_1.7.0.tar.gz
93+
120.08 arrayMagic_1.11.0.tar.gz
94+
118.93 made4_1.7.2.tar.gz
95+
117.10 GEOquery_1.7.0.tar.gz
96+
116.92 nudge_1.3.0.tar.gz
97+
114.82 apComplex_1.7.1.tar.gz
98+
114.11 clusterStab_1.5.0.tar.gz
99+
113.99 sscore_1.5.2.tar.gz
100+
113.89 biocViews_1.1.3.tar.gz
101+
111.58 siggenes_1.7.1.tar.gz
102+
110.23 simpleaffy_2.7.0.tar.gz
103+
109.25 GeneTraffic_1.5.0.tar.gz
104+
108.72 sigPathway_1.1.6.tar.gz
105+
105.77 Biostrings_2.1.4.tar.gz
106+
104.63 spotSegmentation_1.5.0.tar.gz
107+
104.39 splicegear_1.5.0.tar.gz
108+
103.96 maDB_1.5.1.tar.gz
109+
102.17 bridge_1.5.0.tar.gz
110+
100.58 iSPlot_1.7.8.tar.gz
111+
99.71 GLAD_1.7.1.tar.gz
112+
98.99 LPE_1.7.0.tar.gz
113+
97.31 KEGGSOAP_1.7.0.tar.gz
114+
96.85 Rredland_1.1.3.tar.gz
115+
96.47 affylmGUI_1.7.0.tar.gz
116+
93.82 Icens_1.5.0.tar.gz
117+
93.81 idiogram_1.7.0.tar.gz
118+
91.50 RMAGEML_2.7.0.tar.gz
119+
91.27 MANOR_1.5.0.tar.gz
120+
90.82 webbioc_1.5.0.tar.gz
121+
85.82 OLINgui_1.7.0.tar.gz
122+
85.57 metaArray_1.5.1.tar.gz
123+
84.68 GeneR_2.3.0.tar.gz
124+
82.81 SBMLR_1.27.0.tar.gz
125+
82.41 MVCClass_1.7.14.tar.gz
126+
82.05 pairseqsim_1.7.0.tar.gz
127+
81.62 ssize_1.5.0.tar.gz
128+
81.23 logicFS_1.3.1.tar.gz
129+
80.82 quantsmooth_0.9.2.tar.gz
130+
80.21 Harshlight_1.1.2.tar.gz
131+
79.81 hypergraph_1.5.0.tar.gz
132+
79.77 codelink_1.1.3.tar.gz
133+
79.19 pamr_1.31.0.tar.gz
134+
77.65 convert_1.7.0.tar.gz
135+
75.82 plier_1.5.1.tar.gz
136+
74.11 genArise_1.9.0.tar.gz
137+
73.44 exprDB_0.3.0.tar.gz
138+
72.36 oligo_0.99.16.tar.gz
139+
72.08 ABarray_1.1.3.tar.gz
140+
70.82 MeasurementError.cor_1.5.0.tar.gz
141+
69.14 ctc_1.7.0.tar.gz
142+
67.81 gtkWidgets_0.11.0.tar.gz
143+
67.74 bioDist_1.5.0.tar.gz
144+
66.83 CoCiteStats_1.5.1.tar.gz
145+
63.93 HEM_1.5.0.tar.gz
146+
63.80 Mfuzz_1.1.0.tar.gz
147+
62.80 tkWidgets_1.11.2.tar.gz
148+
61.81 rama_1.5.0.tar.gz
149+
60.91 makePlatformDesign_0.99.16.tar.gz
150+
60.32 Heatplus_1.3.1.tar.gz
151+
58.79 maCorrPlot_1.3.0.tar.gz
152+
58.47 GeneSpring_2.5.0.tar.gz
153+
57.85 geneRecommender_1.5.0.tar.gz
154+
52.25 TypeInfo_0.3.1.tar.gz
155+
47.79 widgetTools_1.9.1.tar.gz
156+
47.78 limmaGUI_1.9.0.tar.gz
157+
46.80 widgetInvoke_1.5.0.tar.gz
158+
45.79 prism_0.1.1.tar.gz
159+
45.70 GenomeBase_1.1.0.tar.gz
160+
44.26 ROC_1.7.0.tar.gz
161+
39.96 Ruuid_1.11.1.tar.gz
162+
39.79 gaggle_1.1.5.tar.gz
163+
39.77 DynDoc_1.11.1.tar.gz
164+
37.79 pickgene_1.5.0.tar.gz
165+
35.72 gff3Plotter_1.7.0.tar.gz
166+
33.14 RdbiPgSQL_1.7.2.tar.gz
167+
32.82 GeneRfold_0.1.3.tar.gz
168+
32.78 pgUtils_1.5.0.tar.gz
169+
32.41 affyio_1.1.6.tar.gz
170+
31.91 ChromoViz_1.5.0.tar.gz
171+
31.78 qvalue_1.7.0.tar.gz
172+
30.79 diffGeneAnalysis_1.15.0.tar.gz
173+
30.79 daMA_1.5.0.tar.gz
174+
30.78 RMAPPER_1.3.0.tar.gz
175+
29.78 spikeLI_1.1.0.tar.gz
176+
29.77 impute_1.5.0.tar.gz
177+
28.79 fdrame_1.5.0.tar.gz
178+
27.77 RLMM_0.11.0.tar.gz
179+
27.54 Rdbi_1.7.0.tar.gz
180+
26.79 sizepower_1.3.0.tar.gz
181+
16.75 RPostgreSQL_0.0.0.tar.gz
182+
15.77 GeneTS_2.11.1.tar.gz
183+
13.77 externalVector_1.5.0.tar.gz
184+
6.76 exprExternal_1.5.0.tar.gz
185+
5.76 SNPscan_0.1.17.tar.gz

0 commit comments

Comments
 (0)