Question: Troubles installing pcaMethods on R2.12.1
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gravatar for Manca Marco PATH
8.7 years ago by
Manca Marco PATH340 wrote:
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/contri b/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 ********************************************************************** *********************************************** This email and any files transmitted with it are confide...{{dropped:15}}
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