[BioC] library(\"geneplotter\") fails on load
Ron Eisler [guest]
guest at bioconductor.org
Thu May 16 19:16:53 CEST 2013
Hello,
I know the R code/version I am inquiring about is outdated, unfortunately I am trying to pick up the development thread pieces from someone who passed away several years ago. There are other components of the system integrated into the entire (extremely large and complex) system which disallow upgrading to a current kernel/system. It would require an impossible effort/cost. I am just learning how to work in this environment. I have no option but to make this work.
The distribution in use:
root at cit-calibration: # lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 8.10
Release: 8.10
Codename: intrepid
The error:
root at cit-calibration:# R --vanilla
R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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.
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.
> library("geneplotter")
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) :
in 'geneplotter' methods specified for export, but none defined: Makesense, imageMap
In addition: Warning messages:
1: '.__M__Makesense:geneplotter' looks like a pre-2.4.0 S4 object: please recreate it
2: '.__M__imageMap:geneplotter' looks like a pre-2.4.0 S4 object: please recreate it
3: 'Makesense' looks like a pre-2.4.0 S4 object: please recreate it
4: 'imageMap' looks like a pre-2.4.0 S4 object: please recreate it
Error: package/namespace load failed for 'geneplotter'
I would re-create them, if I could determine how to do it.
I have downloaded the R source and recompiled from scratch. As can be seen from the listing below, the geneplotter directory has not been touched (along with some others). I do not know why.
root at cit-calibration: # ls -ltr /usr/local/lib/R/site-library
drwxr-sr-x 10 root staff 4096 Sep 8 2005 sma
drwxr-sr-x 11 root staff 4096 Sep 8 2005 sfsmisc
drwxr-sr-x 11 root staff 4096 Sep 8 2005 waveslim
drwxr-sr-x 10 root staff 4096 Sep 8 2005 pls.pcr
drwxr-sr-x 12 root staff 4096 Feb 9 2006 vegan
drwxr-sr-x 12 root staff 4096 Feb 9 2006 ade4
drwxr-sr-x 11 root staff 4096 Feb 10 2006 mvpart
drwxr-sr-x 14 root staff 4096 Nov 28 2006 reposTools
drwxr-sr-x 10 root staff 4096 Nov 28 2006 xtable
drwxr-sr-x 11 root staff 4096 Nov 28 2006 annaffy
drwxr-sr-x 11 root staff 4096 Nov 28 2006 annotate
drwxr-sr-x 13 root staff 4096 Nov 28 2006 genefilter
drwxr-sr-x 11 root staff 4096 Nov 28 2006 geneplotter
drwxr-sr-x 17 root staff 4096 May 15 11:51 Biobase
drwxr-sr-x 15 root staff 4096 May 15 11:51 Biostrings
drwxr-sr-x 9 root staff 4096 May 15 11:51 DynDoc
drwxr-sr-x 10 root staff 4096 May 15 11:51 GO
drwxr-sr-x 10 root staff 4096 May 15 11:51 KEGG
drwxr-sr-x 11 root staff 4096 May 15 11:51 KernSmooth
drwxr-sr-x 11 root staff 4096 May 15 11:52 MNP
drwxr-sr-x 12 root staff 4096 May 15 11:52 MatchIt
drwxr-sr-x 9 root staff 4096 May 15 11:52 RColorBrewer
drwxr-sr-x 11 root staff 4096 May 15 11:52 ROC
drwxr-sr-x 13 root staff 4096 May 15 11:52 RUnit
drwxr-sr-x 10 root staff 4096 May 15 11:52 Rserve
drwxr-sr-x 9 root staff 4096 May 15 11:52 abind
drwxr-sr-x 10 root staff 4096 May 15 11:52 acepack
drwxr-sr-x 10 root staff 4096 May 15 11:52 affyio
drwxr-sr-x 10 root staff 4096 May 15 11:52 cclust
drwxr-sr-x 9 root staff 4096 May 15 11:52 codetools
drwxr-sr-x 10 root staff 4096 May 15 11:52 date
drwxr-sr-x 11 root staff 4096 May 15 11:52 eco
drwxr-sr-x 10 root staff 4096 May 15 11:52 getopt
drwxr-sr-x 9 root staff 4096 May 15 11:52 gmodels
drwxr-sr-x 11 root staff 4096 May 15 11:52 gtools
drwxr-sr-x 10 root staff 4096 May 15 11:52 hgu95av2
drwxr-sr-x 10 root staff 4096 May 15 11:52 limma
drwxr-sr-x 10 root staff 4096 May 15 11:53 lpSolve
drwxr-sr-x 10 root staff 4096 May 15 11:53 mapproj
drwxr-sr-x 11 root staff 4096 May 15 11:53 misc3d
drwxr-sr-x 10 root staff 4096 May 15 11:53 mnormt
drwxr-sr-x 11 root staff 4096 May 15 11:53 mvtnorm
drwxr-sr-x 13 root staff 4096 May 15 11:53 nws
drwxr-sr-x 12 root staff 4096 May 15 11:53 permute
drwxr-sr-x 10 root staff 4096 May 15 11:53 polspline
drwxr-sr-x 11 root staff 4096 May 15 11:53 preprocessCore
drwxr-sr-x 10 root staff 4096 May 15 11:53 psy
drwxr-sr-x 9 root staff 4096 May 15 11:53 relimp
drwxr-sr-x 11 root staff 4096 May 15 11:53 sandwich
drwxr-sr-x 13 root staff 4096 May 15 11:53 urca
drwxr-sr-x 13 root staff 4096 May 15 11:54 affy
drwxr-sr-x 9 root staff 4096 May 15 11:54 fBonds
drwxr-sr-x 10 root staff 4096 May 15 11:54 gregmisc
drwxr-sr-x 12 root staff 4096 May 15 11:54 its
drwxr-sr-x 12 root staff 4096 May 15 11:54 marray
drwxr-sr-x 13 root staff 4096 May 15 11:54 multtest
drwxr-sr-x 10 root staff 4096 May 15 11:55 GO.db
drwxr-sr-x 10 root staff 4096 May 15 11:55 KEGG.db
drwxr-sr-x 12 root staff 4096 May 15 11:55 affydata
drwxr-sr-x 10 root staff 4096 May 15 11:55 hgu95av2.db
drwxr-sr-x 15 root staff 4096 May 15 11:55 matchprobes
drwxr-sr-x 13 root staff 4096 May 15 11:55 vsn
drwxr-sr-x 12 root staff 4096 May 15 11:55 gcrma
drwxr-sr-x 11 root staff 4096 May 15 11:55 affyPLM
drwxr-sr-x 12 root staff 4096 May 15 11:55 affyQCReport
-rw-r--r-- 1 root staff 866 May 15 11:55 R.css
Library environment variable:
root at cit-calibration: echo $R_LIBS_SITE
/usr/local/lib/R/site-library
> searchpaths()
[1] ".GlobalEnv" "/usr/lib64/R/library/stats"
[3] "/usr/lib64/R/library/graphics" "/usr/lib64/R/library/grDevices"
[5] "/usr/lib64/R/library/utils" "/usr/lib64/R/library/datasets"
[7] "/usr/lib64/R/library/methods" "Autoloads"
[9] "/usr/lib64/R/library/base"
I have tried this sequence:
> source("http://bioconductor.org/biocLite.R")
> pkgs <- rownames(installed.packages())
> biocLite(pkgs)
which of course downloads and rebuilds all the packages. There were 29 warnings from this procedure.
Running biocinstall version 2.2.11 with R version 2.7.1
Your version of R requires version 2.2 of BioConductor.
Originally I had 29 warnings (several re-attempts):
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
packages ~@~Xade4~@~Y, ~@~Xmvpart~@~Y, ~@~Xpls.pcr~@~Y, ~@~XreposTools~@~Y, ~@~Xsfsmisc~@~Y, ~@~Xsma~@~Y, ~@~Xwaveslim~@~Y, ~@~Xxtable
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
dependencies ~@~XtimeDate~@~Y, ~@~XtimeSeries~@~Y, ~@~Xstabledist~@~Y, ~@~Xgss~@~Y, ~@~XRSQLite~@~Y are not available
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fBasics' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'Hmisc' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'RGtk2' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'rsprng' had non-zero exit status
7: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'XML' had non-zero exit status
8: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'AnnotationDbi' had non-zero exit status
9: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'vegan' had non-zero exit status
10: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fArma' had non-zero exit status
11: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fNonlinear' had non-zero exit status
12: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fOptions' had non-zero exit status
13: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fTrading' had non-zero exit status
14: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fUnitRoots' had non-zero exit status
15: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'multcomp' had non-zero exit status
16: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'rggobi' had non-zero exit status
17: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'sn' had non-zero exit status
18: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'annotate' had non-zero exit status
19: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fAsianOptions' had non-zero exit status
20: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fCopulae' had non-zero exit status
21: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fExoticOptions' had non-zero exit status
22: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fExtremes' had non-zero exit status
23: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fMultivar' had non-zero exit status
24: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'annaffy' had non-zero exit status
25: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'genefilter' had non-zero exit status
26: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'geneplotter' had non-zero exit status
27: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fAssets' had non-zero exit status
28: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fRegression' had non-zero exit status
29: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'simpleaffy' had non-zero exit status
Today I get only 15:
The downloaded packages are in
/tmp/RtmpBQQJea/downloaded_packages
There were 15 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
packages 'ade4', 'mvpart', 'pls.pcr', 'reposTools', 'sfsmisc', 'sma', 'waveslim', 'xtable', 'VR', 'base', 'boot', 'cluster', 'datasets', 'foreign', 'grDevices', 'graphics', 'grid', 'lattice', 'methods', 'mgcv', 'nlme', 'rpart', 'splines', 'stats', 'stats4', 'survival', 'tcltk', 'tools', 'utils' are not available
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
dependencies 'timeDate', 'timeSeries', 'gdata', 'gplots', 'maps', 'zoo', 'DBI', 'RSQLite', 'stabledist', 'gss' are not available
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'fBasics' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'Hmisc' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'Rserve' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'gmodels' had non-zero exit status
7: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'sandwich' had non-zero exit status
8: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'AnnotationDbi' had non-zero exit status
9: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'its' had non-zero exit status
10: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'vegan' had non-zero exit status
11: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'annotate' had non-zero exit status
12: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'annaffy' had non-zero exit status
13: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'genefilter' had non-zero exit status
14: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'geneplotter' had non-zero exit status
15: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... :
installation of package 'simpleaffy' had non-zero exit status
>From the compile:
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265: warning: assignment from incompatible pointer type
fintegrate.c: In function 'paramIntegration':
fintegrate.c:350: warning: ignoring return value of 'scanf', declared with
attribute warn_unused_result
gibbsEM.c: In function 'ecoEStep':
gibbsEM.c:417: warning: ignoring return value of 'scanf', declared with
attribute warn_unused_result
commonlib.c: In function 'blockWriteINT':
commonlib.c:693: warning: format not a string literal and no format arguments
commonlib.c: In function 'blockWriteBOOL':
commonlib.c:712: warning: format not a string literal and no format arguments
commonlib.c: In function 'blockWriteREAL':
commonlib.c:734: warning: format not a string literal and no format arguments
hbio.c: In function 'readHB_info':
hbio.c:265: warning: cast from pointer to integer of different size
hbio.c: In function 'readHB_header':
hbio.c:307: warning: cast from pointer to integer of different size
hbio.c:308: warning: cast from pointer to integer of different size
hbio.c:343: warning: cast from pointer to integer of different size
hbio.c:344: warning: cast from pointer to integer of different size
hbio.c:345: warning: cast from pointer to integer of different size
hbio.c:346: warning: cast from pointer to integer of different size
hbio.c:303: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:311: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:321: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:333: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:351: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c: In function 'readHB_mat_double':
hbio.c:420: warning: cast from pointer to integer of different size
hbio.c:443: warning: cast from pointer to integer of different size
hbio.c:472: warning: cast from pointer to integer of different size
hbio.c:424: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:447: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:476: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c: In function 'readHB_aux_double':
hbio.c:660: warning: cast from pointer to integer of different size
hbio.c:627: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:638: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:645: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:665: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:693: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c: In function 'readHB_mat_char':
hbio.c:974: warning: cast from pointer to integer of different size
hbio.c:997: warning: cast from pointer to integer of different size
hbio.c:1025: warning: cast from pointer to integer of different size
hbio.c:978: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1001: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1029: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c: In function 'readHB_aux_char':
hbio.c:1193: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1204: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1214: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1232: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c:1263: warning: ignoring return value of 'fgets', declared with attribute
warn_unused_result
hbio.c: In function 'ParseRfmt':
hbio.c:1539: warning: cast from pointer to integer of different size
hbio.c:1549: warning: cast from pointer to integer of different size
hbio.c:1553: warning: cast from pointer to integer of different size
hbio.c: In function 'substr':
hbio.c:1587: warning: cast from pointer to integer of different size
lp_lib.c: In function 'read_XLI':
lp_lib.c:5339: warning: implicit declaration of function 'Rprintf'
lp_report.c: In function 'blockWriteLREAL':
lp_report.c:167: warning: format not a string literal and no format arguments
lp_report.c: In function 'blockWriteAMAT':
lp_report.c:196: warning: format not a string literal and no format arguments
lp_report.c: In function 'blockWriteBMAT':
lp_report.c:261: warning: format not a string literal and no format arguments
In file included from lp_rlp.c:97:
lp_rlp.h: In function 'lp_yylex':
lp_rlp.h:1012: warning: ignoring return value of 'fwrite', declared with
attribute warn_unused_result
lusol.c: In function 'LUSOL_report':
lusol.c:626: warning: implicit declaration of function 'REvprintf'
mmio.c: In function 'mm_read_unsymmetric_sparse':
mmio.c:79: warning: ignoring return value of 'fscanf', declared with attribute
warn_unused_result
sparselib.c: In function 'resizeMatrix':
sparselib.c:51: warning: ignoring return value of 'realloc', declared with
attribute warn_unused_result
albers.c:10: warning: type defaults to 'int' in declaration of 'southpole'
The drop in erros might have been due to:
# dpkg --install tex-common
I don't know.
It doesn't seem like I am too far off from running.
Any help is greatly appreciated.
Ron
-- output of sessionInfo():
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-pc-linux-gnu
locale:
C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] annotate_1.5.16 Biobase_2.0.1
loaded via a namespace (and not attached):
[1] KernSmooth_2.23-10 RColorBrewer_1.0-5
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