annmap 1.15.0
Chris Wirth
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annmap | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data annmap
###
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* checking for file ‘annmap/DESCRIPTION’ ... OK
* preparing ‘annmap’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
/Library/Frameworks/R.framework/Resources/bin/R --vanilla --verbose < ../inst/cookbook/delia.R
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/methods/libs/methods.so") ...
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
'verbose' and 'quietly' are both true; being verbose then ..
'verbose' and 'quietly' are both true; being verbose then ..
Garbage collection 1 = 0+0+1 (level 2) ...
5.9 Mbytes of cons cells used (31%)
1.5 Mbytes of vectors used (24%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/utils/libs/utils.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/grDevices/libs/grDevices.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
Garbage collection 2 = 1+0+1 (level 0) ...
10.4 Mbytes of cons cells used (55%)
2.4 Mbytes of vectors used (39%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/graphics/libs/graphics.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
Garbage collection 3 = 2+0+1 (level 0) ...
11.3 Mbytes of cons cells used (60%)
2.5 Mbytes of vectors used (41%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/stats/libs/stats.so") ...
ending setup_Rmainloop(): R_Interactive = 0 {main.c}
>R_ReplConsole(): before "for(;;)" {main.c}
> # This script builds the cookbook if the correct DB name is set up
> # Or else does nothing, and leaves the PDF where it is...
> #
> # http://bit.ly/delia_smith
>
> library( "annmap" )
Loading required package: GenomicRanges
Loading required package: stats4
Garbage collection 4 = 3+0+1 (level 0) ...
13.2 Mbytes of cons cells used (71%)
2.9 Mbytes of vectors used (48%)
Garbage collection 5 = 4+0+1 (level 0) ...
14.9 Mbytes of cons cells used (80%)
3.3 Mbytes of vectors used (54%)
Loading required package: BiocGenerics
Loading required package: parallel
Garbage collection 6 = 5+0+1 (level 0) ...
15.2 Mbytes of cons cells used (81%)
3.3 Mbytes of vectors used (55%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/parallel/libs/parallel.so") ...
Garbage collection 7 = 5+1+1 (level 1) ...
15.6 Mbytes of cons cells used (83%)
3.2 Mbytes of vectors used (52%)
Garbage collection 8 = 5+1+2 (level 2) ...
15.9 Mbytes of cons cells used (64%)
3.2 Mbytes of vectors used (41%)
Garbage collection 9 = 6+1+2 (level 0) ...
16.7 Mbytes of cons cells used (68%)
3.4 Mbytes of vectors used (43%)
Garbage collection 10 = 7+1+2 (level 0) ...
17.8 Mbytes of cons cells used (72%)
3.7 Mbytes of vectors used (46%)
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Garbage collection 11 = 8+1+2 (level 0) ...
18.8 Mbytes of cons cells used (76%)
3.9 Mbytes of vectors used (49%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs/S4Vectors.so") ...
Garbage collection 12 = 9+1+2 (level 0) ...
20.8 Mbytes of cons cells used (85%)
4.1 Mbytes of vectors used (52%)
Garbage collection 13 = 9+2+2 (level 1) ...
21.9 Mbytes of cons cells used (89%)
4.2 Mbytes of vectors used (53%)
Garbage collection 14 = 9+2+3 (level 2) ...
21.8 Mbytes of cons cells used (69%)
4.1 Mbytes of vectors used (52%)
Garbage collection 15 = 10+2+3 (level 0) ...
22.0 Mbytes of cons cells used (69%)
4.2 Mbytes of vectors used (53%)
Garbage collection 16 = 11+2+3 (level 0) ...
22.0 Mbytes of cons cells used (69%)
4.2 Mbytes of vectors used (53%)
Garbage collection 17 = 12+2+3 (level 0) ...
22.0 Mbytes of cons cells used (69%)
4.2 Mbytes of vectors used (53%)
Garbage collection 18 = 13+2+3 (level 0) ...
22.0 Mbytes of cons cells used (69%)
4.2 Mbytes of vectors used (53%)
Garbage collection 19 = 14+2+3 (level 0) ...
22.0 Mbytes of cons cells used (69%)
4.2 Mbytes of vectors used (53%)
Garbage collection 20 = 15+2+3 (level 0) ...
22.2 Mbytes of cons cells used (70%)
4.2 Mbytes of vectors used (53%)
Garbage collection 21 = 16+2+3 (level 0) ...
22.2 Mbytes of cons cells used (70%)
4.2 Mbytes of vectors used (53%)
Garbage collection 22 = 17+2+3 (level 0) ...
23.5 Mbytes of cons cells used (74%)
4.3 Mbytes of vectors used (54%)
Garbage collection 23 = 18+2+3 (level 0) ...
25.3 Mbytes of cons cells used (80%)
4.6 Mbytes of vectors used (58%)
Garbage collection 24 = 19+2+3 (level 0) ...
26.0 Mbytes of cons cells used (82%)
4.7 Mbytes of vectors used (59%)
Garbage collection 25 = 19+3+3 (level 1) ...
26.4 Mbytes of cons cells used (83%)
4.7 Mbytes of vectors used (59%)
Garbage collection 26 = 19+3+4 (level 2) ...
27.0 Mbytes of cons cells used (67%)
4.8 Mbytes of vectors used (47%)
Garbage collection 27 = 20+3+4 (level 0) ...
29.0 Mbytes of cons cells used (72%)
5.1 Mbytes of vectors used (50%)
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Garbage collection 28 = 20+4+4 (level 1) ...
29.9 Mbytes of cons cells used (74%)
5.3 Mbytes of vectors used (52%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/libs/IRanges.so") ...
Garbage collection 29 = 21+4+4 (level 0) ...
32.7 Mbytes of cons cells used (81%)
5.5 Mbytes of vectors used (55%)
Garbage collection 30 = 21+5+4 (level 1) ...
35.7 Mbytes of cons cells used (89%)
5.6 Mbytes of vectors used (56%)
Garbage collection 31 = 21+5+5 (level 2) ...
35.3 Mbytes of cons cells used (70%)
5.5 Mbytes of vectors used (55%)
Garbage collection 32 = 22+5+5 (level 0) ...
35.4 Mbytes of cons cells used (70%)
5.5 Mbytes of vectors used (55%)
Garbage collection 33 = 23+5+5 (level 0) ...
35.4 Mbytes of cons cells used (70%)
5.5 Mbytes of vectors used (55%)
Garbage collection 34 = 24+5+5 (level 0) ...
35.8 Mbytes of cons cells used (71%)
5.5 Mbytes of vectors used (55%)
Garbage collection 35 = 25+5+5 (level 0) ...
35.8 Mbytes of cons cells used (71%)
5.6 Mbytes of vectors used (55%)
Garbage collection 36 = 26+5+5 (level 0) ...
40.4 Mbytes of cons cells used (80%)
5.9 Mbytes of vectors used (58%)
Garbage collection 37 = 26+5+6 (level 2) ...
41.4 Mbytes of cons cells used (66%)
6.0 Mbytes of vectors used (47%)
Garbage collection 38 = 27+5+6 (level 0) ...
45.6 Mbytes of cons cells used (73%)
6.4 Mbytes of vectors used (50%)
Garbage collection 39 = 28+5+6 (level 0) ...
49.0 Mbytes of cons cells used (78%)
6.7 Mbytes of vectors used (53%)
Loading required package: GenomeInfoDb
Garbage collection 40 = 29+5+6 (level 0) ...
49.3 Mbytes of cons cells used (79%)
6.8 Mbytes of vectors used (54%)
Garbage collection 41 = 30+5+6 (level 0) ...
52.6 Mbytes of cons cells used (84%)
7.2 Mbytes of vectors used (57%)
Garbage collection 42 = 30+6+6 (level 1) ...
53.1 Mbytes of cons cells used (85%)
7.1 Mbytes of vectors used (56%)
Garbage collection 43 = 30+6+7 (level 2) ...
52.5 Mbytes of cons cells used (68%)
7.0 Mbytes of vectors used (55%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/libs/XVector.so") ...
Garbage collection 44 = 31+6+7 (level 0) ...
53.7 Mbytes of cons cells used (70%)
7.2 Mbytes of vectors used (57%)
Garbage collection 45 = 32+6+7 (level 0) ...
60.1 Mbytes of cons cells used (78%)
7.6 Mbytes of vectors used (60%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/GenomicRanges/libs/GenomicRanges.so") ...
Garbage collection 46 = 33+6+7 (level 0) ...
61.4 Mbytes of cons cells used (80%)
7.7 Mbytes of vectors used (61%)
Garbage collection 47 = 34+6+7 (level 0) ...
66.6 Mbytes of cons cells used (86%)
8.0 Mbytes of vectors used (63%)
Garbage collection 48 = 34+7+7 (level 1) ...
70.7 Mbytes of cons cells used (92%)
8.2 Mbytes of vectors used (65%)
Garbage collection 49 = 34+7+8 (level 2) ...
70.2 Mbytes of cons cells used (74%)
8.1 Mbytes of vectors used (51%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/grid/libs/grid.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biobase/libs/Biobase.so") ...
Garbage collection 50 = 35+7+8 (level 0) ...
72.6 Mbytes of cons cells used (77%)
8.5 Mbytes of vectors used (54%)
Garbage collection 51 = 36+7+8 (level 0) ...
75.8 Mbytes of cons cells used (80%)
8.8 Mbytes of vectors used (56%)
Garbage collection 52 = 36+8+8 (level 1) ...
76.0 Mbytes of cons cells used (80%)
8.8 Mbytes of vectors used (56%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bitops/libs/bitops.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RCurl/libs/RCurl.so") ...
Garbage collection 53 = 36+8+9 (level 2) ...
78.6 Mbytes of cons cells used (68%)
9.0 Mbytes of vectors used (57%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XML/libs/XML.so") ...
Garbage collection 54 = 37+8+9 (level 0) ...
83.0 Mbytes of cons cells used (72%)
9.5 Mbytes of vectors used (60%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RSQLite/libs/RSQLite.so") ...
Garbage collection 55 = 38+8+9 (level 0) ...
85.0 Mbytes of cons cells used (74%)
9.8 Mbytes of vectors used (62%)
Garbage collection 56 = 39+8+9 (level 0) ...
89.7 Mbytes of cons cells used (78%)
10.2 Mbytes of vectors used (65%)
Garbage collection 57 = 40+8+9 (level 0) ...
92.4 Mbytes of cons cells used (80%)
10.5 Mbytes of vectors used (66%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/splines/libs/splines.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/lattice/libs/lattice.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Matrix/libs/Matrix.so") ...
Garbage collection 58 = 40+9+9 (level 1) ...
97.2 Mbytes of cons cells used (84%)
10.9 Mbytes of vectors used (69%)
Garbage collection 59 = 40+9+10 (level 2) ...
103.0 Mbytes of cons cells used (73%)
11.1 Mbytes of vectors used (57%)
Garbage collection 60 = 41+9+10 (level 0) ...
107.7 Mbytes of cons cells used (76%)
11.2 Mbytes of vectors used (57%)
Garbage collection 61 = 42+9+10 (level 0) ...
108.2 Mbytes of cons cells used (77%)
11.3 Mbytes of vectors used (58%)
Garbage collection 62 = 43+9+10 (level 0) ...
114.0 Mbytes of cons cells used (81%)
11.5 Mbytes of vectors used (59%)
Garbage collection 63 = 43+10+10 (level 1) ...
123.8 Mbytes of cons cells used (88%)
12.0 Mbytes of vectors used (61%)
Garbage collection 64 = 43+10+11 (level 2) ...
128.2 Mbytes of cons cells used (75%)
12.4 Mbytes of vectors used (63%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/survival/libs/survival.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/genefilter/libs/genefilter.so") ...
Garbage collection 65 = 44+10+11 (level 0) ...
134.5 Mbytes of cons cells used (79%)
13.0 Mbytes of vectors used (66%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/libs/Biostrings.so") ...
Garbage collection 66 = 45+10+11 (level 0) ...
138.9 Mbytes of cons cells used (81%)
13.3 Mbytes of vectors used (68%)
Garbage collection 67 = 45+10+12 (level 2) ...
144.5 Mbytes of cons cells used (70%)
13.6 Mbytes of vectors used (56%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/libs/Rsamtools.so") ...
Garbage collection 68 = 46+10+12 (level 0) ...
153.3 Mbytes of cons cells used (74%)
14.3 Mbytes of vectors used (59%)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RMySQL/libs/RMySQL.so") ...
now dyn.load("/Library/Frameworks/R.framework/Versions/3.3/Resources/library/digest/libs/digest.so") ...
>
> data = tryCatch( annmapConnect( "hs-test" ), error=function(e) { FALSE } )
Using /Users/biocbuild/.annmap as our configuration directory.
> if( length( data ) == 1 ) {
+ # The here's one I prepared earlier shortcut
+ message( "Cannot find datasource 'hs-test', I'm not going to build the cookbook." )
+ } else {
+ message( "Generating cookbook..." )
+ # First, we'll disconnect, so the Rnw gets a fresh start
+ annmapDisconnect()
+
+ current.path = getwd()
+ path <- file.path( getwd(), "..", "inst/cookbook" )
+ setwd( path )
+ # Parse the Rnw
+ library(tools)
+ utils::Sweave( 'cookbook.Rnw' )
+
+ # Generate the PDF
+ texi2dvi( 'cookbook.tex', pdf=T, clean=T )
+
+ # Copy it to the docs
+ file.copy( 'cookbook.pdf', file.path( path, '../..', 'vignettes' ), overwrite=T )
+
+ # cleanup
+ unlink( 'cookbook.pdf' )
+ unlink( 'cookbook.tex' )
+ unlink( 'bridge1.png' )
+ unlink( 'bridge2.png' )
+ unlink( 'bridge3.png' )
+ unlink( 'bridge4.png' )
+ unlink( 'bridge5.png' )
+ unlink( 'gviz1.png' )
+ unlink( 'fig1.pdf' )
+ unlink( 'fig2.pdf' )
+ unlink( 'fig3.pdf' )
+ unlink( 'fig4.pdf' )
+ unlink( 'fig5.pdf' )
+ unlink( 'fig6.pdf' )
+ unlink( 'fig7.pdf' )
+ unlink( 'fig8.pdf' )
+ unlink( 'fig9.pdf' )
+ unlink( 'fig10.pdf' )
+
+ setwd( current.path )
+ }
Cannot find datasource 'hs-test', I'm not going to build the cookbook.
>
>
texi2dvi --pdf annmap.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
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entering extended mode
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==> Fatal error occurred, no output PDF file produced!
Transcript written on annmap.log.
/usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/bin/texi2dvi: see annmap.log for errors.
make: *** [pdf] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted