icc has not previously been supported. I am planning to investigate how to improve the codes portability. Ben -----Original Message----- From: Dan Tenenbaum Sent: Monday, November 29, 2010 10:42 AM To: Zhenguo Zhang ; Ben Bolstad Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Can not install 'affyio' with compiler icc on redhatlinux ES5 On Wed, Nov 24, 2010 at 3:34 PM, Zhenguo Zhang <zuz17 at="" psu.edu=""> wrote: > Dear Colleagues, > > I am installing package 'affyio' on our sever with biocLite("affyio") > command. > The compiler is icc (intel/11.1.073), and the R version is R/2.12.0. I > have > also tried to install it by using other versions of R and icc. All failed > with > the same reason. See the following error messages. I also tried several > other > bioconductor packages, such as GOStats. It works. If anyone has some > experience > about this, please help me. Thanks so much. > > I'm cc'ing the maintainer of affyio who can tell us whether this compiler is supported. Thanks Dan > Have a good thanksgiving day! > > Error messages: > > > R version 2.12.0 (2010-10-15) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-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. > > Loading required package: utils > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > > Welcome at Wed Nov 24 18:11:52 2010 > > source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > > biocLite("affyio") > Using R version 2.12.0, biocinstall version 2.7.4. > Installing Bioconductor version 2.7 packages: > [1] "affyio" > Please wait... > > Installing package(s) into ?/gpfs/home/zuz17/Scripts/R/lib? > (as ?lib? is unspecified) > trying URL > ' > http://www.bioconductor.org/packages/2.7/bioc/src/contrib/affyio_1.1 8.0.tar.gz > ' > Content type 'application/x-gzip' length 112026 bytes (109 Kb) > opened URL > ================================================== > downloaded 109 Kb > > Loading required package: utils > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > > Welcome at Wed Nov 24 18:12:33 2010 > * installing *source* package ?affyio? ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for main in -lz... yes > checking zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > checking if zlib version >= 1.1.3... yes > checking for pthread_create in -lpthread... yes > checking if we can use pthreads... yes > checking if PTHREAD_STACK_MIN is defined... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > icc -std=c99 -I/usr/global/R/2.12.0/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 > -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 > -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include > -g > -O2 -fpic -i-dynamic -mieee-fp -prec-div -O2 > -axSSE2,SSE3,SSEE3,SSE4.1,SSE4.2,AVX -c fread_functions.c -o > fread_functions.o > icc -std=c99 -I/usr/global/R/2.12.0/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 > -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 > -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include > -g > -O2 -fpic -i-dynamic -mieee-fp -prec-div -O2 > -axSSE2,SSE3,SSEE3,SSE4.1,SSE4.2,AVX -c read_abatch.c -o read_abatch.o > read_abatch.c(304): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(str,delimiters,&tmp_pointer); > ^ > > read_abatch.c(304): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(str,delimiters,&tmp_pointer); > ^ > > read_abatch.c(316): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL,delimiters,&tmp_pointer); > ^ > > read_abatch.c(589): warning #266: function "strncasecmp" declared > implicitly > if > (strncasecmp(get_token(cur_tokenset,i),ref_cdfName,strlen(ref_cdfNam e)) == > 0){ > ^ > > read_abatch.c(589): warning #167: argument of type "const char *" is > incompatible with parameter of type "void *" > if > (strncasecmp(get_token(cur_tokenset,i),ref_cdfName,strlen(ref_cdfNam e)) == > 0){ > ^ > > read_abatch.c(648): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(648): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(659): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(671): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(756): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(756): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(767): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(778): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(788): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(862): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(862): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(872): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(884): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(896): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(907): warning #967: conversion from "int" to "char *"; sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1493): warning #266: function "strncasecmp" declared > implicitly > if > (strncasecmp(get_token(cur_tokenset,i),ref_cdfName,strlen(ref_cdfNam e)) == > 0){ > ^ > > read_abatch.c(1493): warning #167: argument of type "const char *" is > incompatible with parameter of type "void *" > if > (strncasecmp(get_token(cur_tokenset,i),ref_cdfName,strlen(ref_cdfNam e)) == > 0){ > ^ > > read_abatch.c(1549): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1549): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1560): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1571): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1646): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1646): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1658): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1670): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1682): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1751): warning #266: function "strtok_r" declared implicitly > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1751): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(buffer," \t",&tmp_pointer); > ^ > > read_abatch.c(1761): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1772): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1783): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(1793): warning #967: conversion from "int" to "char *"; > sizes > do not match > current_token = strtok_r(NULL," \t",&tmp_pointer); > ^ > > read_abatch.c(2805): warning #266: function "strncasecmp" declared > implicitly > if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){ > ^ > > read_abatch.c(2805): warning #167: argument of type "const char *" is > incompatible with parameter of type "void *" > if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){ > ^ > > read_abatch.c(3544): warning #266: function "strncasecmp" declared > implicitly > if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){ > ^ > > read_abatch.c(3544): warning #167: argument of type "const char *" is > incompatible with parameter of type "void *" > if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){ > ^ > > read_abatch.c(4376): warning #1011: missing return statement at end of > non-void function "readfile_group" > } > ^ > > read_abatch.c(4385): warning #1011: missing return statement at end of > non-void function "checkFileCDF_group" > } > ^ > > read_abatch.c(4449): error: identifier "PTHREAD_STACK_MIN" is undefined > size_t stacksize = PTHREAD_STACK_MIN + 0x40000; > ^ > > compilation aborted for read_abatch.c (code 2) > make: *** [read_abatch.o] Error 2 > ERROR: compilation failed for package ?affyio? > * removing ?/gpfs/home/zuz17/Scripts/R/lib/affyio? > > The downloaded packages are in > ?/tmp/RtmppB6Zeo/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'affyio' had non-zero exit status > > > > Goodbye at Wed Nov 24 18:12:41 2010 > > > ************************************************************** > Zhenguo Zhang > Postdoctoral Scholar > 312 Mueller Lab > Institute of Molecular Evolutionary Genetics > Penn State University > Tel: 814-865-2796 > Homepage: <http: www.personal.psu.edu="" zuz17=""/> > Lab page: <http: homes.bio.psu.edu="" people="" faculty="" nei=""/> > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor