Question: Can not install 'affyio' with compiler icc on redhat linux ES5
0
gravatar for Zhenguo Zhang
8.9 years ago by
Zhenguo Zhang10 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. 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_1.18 .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 _cdfName)) == 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 _cdfName)) == 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 _cdfName)) == 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 _cdfName)) == 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]]
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ADD COMMENTlink modified 3.3 years ago by dave10 • written 8.9 years ago by Zhenguo Zhang10
Answer: Can not install 'affyio' with compiler icc on redhat linux ES5
0
gravatar for Dan Tenenbaum
8.9 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Wed, Nov 24, 2010 at 3:34 PM, Zhenguo Zhang <zuz17@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@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]]
ADD COMMENTlink written 8.9 years ago by Dan Tenenbaum8.2k
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
ADD REPLYlink written 8.9 years ago by Ben Bolstad1.2k
Answer: Can not install 'affyio' with compiler icc on redhat linux ES5
0
gravatar for dave
3.3 years ago by
dave10
United States
dave10 wrote:

Dragging up an old thread, but this issue exists for us when using Intel Composer XE 2015 to build our R install for our HPC system, so thought I'd note it here as this thread is the top google result.

Simple fix is to edit the code to set PTHREAD_STACK_MIN to 16384  - which is the default in Linux headers (4 * 4K pages on x86 x86_64)

See:

https://github.com/bmbolstad/affyio/pull/1

https://github.com/dctrud/affyio/tree/icc

Cheers,

DT

ADD COMMENTlink written 3.3 years ago by dave10
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