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### Running command:
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### /home/biocbuild/R/R-4.3.0/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
--- re-building ‘INSTALL.Rnw’ using Sweave
--- finished re-building ‘INSTALL.Rnw’
--- re-building ‘annmap.Rnw’ using Sweave
--- finished re-building ‘annmap.Rnw’
--- re-building ‘cookbook.Rnw’ using Sweave
--- finished re-building ‘cookbook.Rnw’
/home/biocbuild/R/R-4.3.0/bin/R --vanilla --verbose < ../inst/cookbook/delia.R
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/home/biocbuild/R/R-4.3.0/library/methods/libs/methods.so") ...
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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) ...
12.5 Mbytes of cons cells used (35%)
3.2 Mbytes of vectors used (5%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/utils/libs/utils.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/home/biocbuild/R/R-4.3.0/library/grDevices/libs/grDevices.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/home/biocbuild/R/R-4.3.0/library/graphics/libs/graphics.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/home/biocbuild/R/R-4.3.0/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 2 = 1+0+1 (level 0) ...
19.2 Mbytes of cons cells used (54%)
5.4 Mbytes of vectors used (8%)
Loading required package: BiocGenerics
Garbage collection 3 = 2+0+1 (level 0) ...
22.2 Mbytes of cons cells used (62%)
6.2 Mbytes of vectors used (10%)
Garbage collection 4 = 3+0+1 (level 0) ...
24.2 Mbytes of cons cells used (68%)
6.8 Mbytes of vectors used (11%)
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/libs/S4Vectors.so") ...
Garbage collection 5 = 4+0+1 (level 0) ...
27.9 Mbytes of cons cells used (78%)
7.6 Mbytes of vectors used (12%)
Garbage collection 6 = 5+0+1 (level 0) ...
30.7 Mbytes of cons cells used (86%)
8.2 Mbytes of vectors used (13%)
Garbage collection 7 = 5+1+1 (level 1) ...
32.0 Mbytes of cons cells used (90%)
8.0 Mbytes of vectors used (12%)
Garbage collection 8 = 5+1+2 (level 2) ...
32.2 Mbytes of cons cells used (43%)
8.0 Mbytes of vectors used (12%)
Garbage collection 9 = 6+1+2 (level 0) ...
32.4 Mbytes of cons cells used (44%)
8.1 Mbytes of vectors used (13%)
Garbage collection 10 = 7+1+2 (level 0) ...
37.6 Mbytes of cons cells used (51%)
9.3 Mbytes of vectors used (14%)
Garbage collection 11 = 8+1+2 (level 0) ...
44.9 Mbytes of cons cells used (60%)
11.0 Mbytes of vectors used (17%)
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/IRanges/libs/IRanges.so") ...
Garbage collection 12 = 9+1+2 (level 0) ...
58.5 Mbytes of cons cells used (79%)
14.4 Mbytes of vectors used (22%)
Garbage collection 13 = 10+1+2 (level 0) ...
58.9 Mbytes of cons cells used (79%)
14.4 Mbytes of vectors used (22%)
Garbage collection 14 = 11+1+2 (level 0) ...
58.9 Mbytes of cons cells used (79%)
14.4 Mbytes of vectors used (22%)
Garbage collection 15 = 12+1+2 (level 0) ...
58.9 Mbytes of cons cells used (79%)
14.4 Mbytes of vectors used (22%)
Garbage collection 16 = 13+1+2 (level 0) ...
59.5 Mbytes of cons cells used (80%)
14.6 Mbytes of vectors used (23%)
Garbage collection 17 = 13+2+2 (level 1) ...
64.9 Mbytes of cons cells used (87%)
16.5 Mbytes of vectors used (26%)
Garbage collection 18 = 13+2+3 (level 2) ...
65.7 Mbytes of cons cells used (46%)
16.0 Mbytes of vectors used (25%)
Loading required package: GenomeInfoDb
now dyn.load("/home/biocbuild/R/R-4.3.0/library/bitops/libs/bitops.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/RCurl/libs/RCurl.so") ...
Garbage collection 19 = 14+2+3 (level 0) ...
88.0 Mbytes of cons cells used (62%)
21.6 Mbytes of vectors used (34%)
Garbage collection 20 = 15+2+3 (level 0) ...
95.8 Mbytes of cons cells used (68%)
23.7 Mbytes of vectors used (37%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/tools/libs/tools.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/XVector/libs/XVector.so") ...
Garbage collection 21 = 16+2+3 (level 0) ...
105.8 Mbytes of cons cells used (75%)
26.2 Mbytes of vectors used (41%)
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/GenomicRanges/libs/GenomicRanges.so") ...
Garbage collection 22 = 17+2+3 (level 0) ...
118.4 Mbytes of cons cells used (84%)
29.4 Mbytes of vectors used (46%)
Garbage collection 23 = 17+3+3 (level 1) ...
128.9 Mbytes of cons cells used (91%)
31.8 Mbytes of vectors used (50%)
Garbage collection 24 = 17+3+4 (level 2) ...
129.9 Mbytes of cons cells used (47%)
31.9 Mbytes of vectors used (50%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/grid/libs/grid.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/matrixStats/libs/matrixStats.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/Biobase/libs/Biobase.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/XML/libs/XML.so") ...
Garbage collection 25 = 18+3+4 (level 0) ...
148.2 Mbytes of cons cells used (53%)
36.3 Mbytes of vectors used (57%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/bit/libs/bit.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/bit64/libs/bit64.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/rlang/libs/rlang.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/cli/libs/cli.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/vctrs/libs/vctrs.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/RSQLite/libs/RSQLite.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/fastmap/libs/fastmap.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/cachem/libs/cachem.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/png/libs/png.so") ...
Garbage collection 26 = 19+3+4 (level 0) ...
162.6 Mbytes of cons cells used (59%)
39.7 Mbytes of vectors used (62%)
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/Biostrings/libs/Biostrings.so") ...
Garbage collection 27 = 20+3+4 (level 0) ...
179.4 Mbytes of cons cells used (65%)
43.8 Mbytes of vectors used (68%)
Garbage collection 28 = 20+4+4 (level 1) ...
191.6 Mbytes of cons cells used (69%)
46.6 Mbytes of vectors used (73%)
Garbage collection 29 = 21+4+4 (level 0) ...
202.2 Mbytes of cons cells used (73%)
49.2 Mbytes of vectors used (77%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/splines/libs/splines.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/lattice/libs/lattice.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/Matrix/libs/Matrix.so") ...
Garbage collection 30 = 22+4+4 (level 0) ...
214.2 Mbytes of cons cells used (77%)
52.1 Mbytes of vectors used (81%)
Garbage collection 31 = 22+5+4 (level 1) ...
222.9 Mbytes of cons cells used (80%)
54.3 Mbytes of vectors used (85%)
Garbage collection 32 = 22+5+5 (level 2) ...
228.0 Mbytes of cons cells used (49%)
55.8 Mbytes of vectors used (67%)
Garbage collection 33 = 23+5+5 (level 0) ...
246.4 Mbytes of cons cells used (53%)
63.4 Mbytes of vectors used (76%)
Garbage collection 34 = 24+5+5 (level 0) ...
265.0 Mbytes of cons cells used (57%)
67.1 Mbytes of vectors used (81%)
now dyn.load("/home/biocbuild/R/R-4.3.0/library/survival/libs/survival.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/genefilter/libs/genefilter.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/parallel/libs/parallel.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/BiocParallel/libs/BiocParallel.so") ...
Garbage collection 35 = 24+5+6 (level 2) ...
275.7 Mbytes of cons cells used (59%)
67.1 Mbytes of vectors used (67%)
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/Rsamtools/libs/Rsamtools.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/site-library/RMySQL/libs/RMySQL.so") ...
now dyn.load("/home/biocbuild/R/R-4.3.0/library/digest/libs/digest.so") ...
There were 30 warnings (use warnings() to see them)
>
> data = tryCatch( annmapConnect( "hs-test" ), error=function(e) { FALSE } )
Using /home/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
make: texi2dvi: No such file or directory
make: *** [Makefile:8: pdf] Error 127
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted