Hello, I know the R code/version I am inquiring about is outdated, unfortunately I am trying to pick up the development thread pieces from someone who passed away several years ago.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 -- Sent via the guest posting facility at bioconductor.org.