[BioC] Can not install 'affyio' with compiler icc on redhatlinux ES5
Ben Bolstad
bmb at bmbolstad.com
Tue Nov 30 03:42:21 CET 2010
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_1.18.0.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/>
>
>
>
>
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>
>
> _______________________________________________
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