[BioC] Troubles installing pcaMethods on R2.12.1

[Manca Marco (PATH)]

Dear Wolfram,

good evening.

I would like to highlight to your attention an issue that I am experiencing trying to install your pcaMethods package on R 2.12.1 on my new Fedora14 64 bit workstation (at the bottom is my sessionInfo() ). Following is my code:


| > biocLite("pcaMethods")
| Using R version 2.12.1, biocinstall version 2.7.4.
| Installing Bioconductor version 2.7 packages:
| [1] "pcaMethods"
| Please wait...
|
| Installing package(s) into ‘/usr/lib64/R/library’
| (as ‘lib’ is unspecified)
| trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/pcaMethods_1.32.0.tar.gz'
| Content type 'application/x-gzip' length 467350 bytes (456 Kb)
| opened URL
| ==================================================
| downloaded 456 Kb
|
| * installing *source* package ‘pcaMethods’ ...
| ** libs
| g++ -m64 -I/usr/include/R -I/usr/lib64/R/library/Rcpp/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c nipals.cpp -o nipals.o
| nipals.cpp: In function ‘SEXPREC* Nipals(SEXPREC*, SEXPREC*)’:
| nipals.cpp:37:5: error: ‘RcppParams’ was not declared in this scope
| nipals.cpp:37:16: error: expected ‘;’ before ‘rparams’
| nipals.cpp:38:20: error: ‘rparams’ was not declared in this scope
| nipals.cpp:42:5: error: ‘RcppMatrix’ was not declared in this scope
| nipals.cpp:42:16: error: expected primary-expression before ‘double’
| nipals.cpp:42:16: error: expected ‘;’ before ‘double’
| nipals.cpp:43:16: error: expected primary-expression before ‘double’
| nipals.cpp:43:16: error: expected ‘;’ before ‘double’
| nipals.cpp:44:14: error: ‘mat’ was not declared in this scope
| nipals.cpp:46:16: error: expected primary-expression before ‘double’
| nipals.cpp:46:16: error: expected ‘;’ before ‘double’
| nipals.cpp:47:16: error: expected primary-expression before ‘double’
| nipals.cpp:47:16: error: expected ‘;’ before ‘double’
| nipals.cpp:48:16: error: expected primary-expression before ‘double’
| nipals.cpp:48:16: error: expected ‘;’ before ‘double’
| nipals.cpp:120:18: error: ‘est_mat’ was not declared in this scope
| nipals.cpp:121:20: error: ‘omat’ was not declared in this scope
| nipals.cpp:130:9: error: ‘tt’ was not declared in this scope
| nipals.cpp:133:9: error: ‘pp’ was not declared in this scope
| nipals.cpp:146:5: error: ‘RcppResultSet’ was not declared in this scope
| nipals.cpp:146:19: error: expected ‘;’ before ‘rs’
| nipals.cpp:148:18: error: expected primary-expression before ‘double’
| nipals.cpp:148:18: error: expected ‘;’ before ‘double’
| nipals.cpp:149:18: error: expected primary-expression before ‘double’
| nipals.cpp:149:18: error: expected ‘;’ before ‘double’
| nipals.cpp:152:11: error: ‘ttt’ was not declared in this scope
| nipals.cpp:152:21: error: ‘tt’ was not declared in this scope
| nipals.cpp:157:11: error: ‘ppp’ was not declared in this scope
| nipals.cpp:157:21: error: ‘pp’ was not declared in this scope
| nipals.cpp:160:7: error: ‘rs’ was not declared in this scope
| nipals.cpp:160:24: error: ‘ttt’ was not declared in this scope
| nipals.cpp:161:26: error: ‘ppp’ was not declared in this scope
| nipals.cpp:163:7: error: ‘rs’ was not declared in this scope
| nipals.cpp:163:24: error: ‘tt’ was not declared in this scope
| nipals.cpp:164:26: error: ‘pp’ was not declared in this scope
| nipals.cpp:166:5: error: ‘rs’ was not declared in this scope
| nipals.cpp:170:69: error: ‘copyMessageToR’ was not declared in this scope
| nipals.cpp:172:53: error: ‘copyMessageToR’ was not declared in this scope
| nipals.cpp:175:45: error: ‘copyMessageToR’ was not declared in this scope
| nipals.cpp:177:51: error: ‘copyMessageToR’ was not declared in this scope
| make: *** [nipals.o] Error 1
| ERROR: compilation failed for package ‘pcaMethods’
| * removing ‘/usr/lib64/R/library/pcaMethods’
|
| The downloaded packages are in
|     ‘/tmp/Rtmp2CpD91/downloaded_packages’
| Updating HTML index of packages in '.Library'
| Warning message:
| In install.packages(pkgs = pkgs, repos = repos, ...) :
|   installation of package 'pcaMethods' had non-zero exit status



According to the authors of Rcpp the problem arises because your package is not compatible with the last stable version of Rcpp (0.9.0), although BioConductor has download and installed this one as a dependency. Are you planning an update or is the package deprecated?

All the best, Marco



| > sessionInfo()
| R version 2.12.1 (2010-12-16)
| Platform: x86_64-redhat-linux-gnu (64-bit)
|
| locale:
|  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
|  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
|  [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
|  [7] LC_PAPER=en_GB.utf8       LC_NAME=C
|  [9] LC_ADDRESS=C              LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base


--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX Maastricht

E-mail: m.manca at maastrichtuniversity.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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