RSEM installation on mac os x

[Jean Keller]

Hello everyone,

I am a new user of RSEM and I tried to install this program on a IMac (OS X El Capitan 10.11.3). However, when I type the make command I obtain a fatal error :

g++ -std=gnu++98 -Wall -I. -I. -Isamtools-1.3/htslib-1.3  -O3 -c -o extractRef.o extractRef.cpp

extractRef.cpp:1:17: fatal error: cstdio: No such file or directory

 #include<cstdio>

                 ^

compilation terminated.

make: *** [extractRef.o] Error 1

Somebody could help me ?

Thank you in advance,

Jean

[Bo Li]

Hi Jean,

Can you check if you have Xcode installed?

Best,
Bo

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[Jean Keller]

Dear Bo,

Thank you for your quick answer.
I have the latest version of xcode installed (7.2.1). Recently, I experienced some compilation troubles due to clang Apple compiler. On the last program, I solved the problem by typing "export cc=clang", however it did not work for RSEM.

Best,

Jean

[Jean Keller]

Hi,

I tried to install RSEM on a MacBook Pro with the same version of El Capitan and it worked. Howeve, the rsem-run-ebseq command is not installed. Consequently, my questions are :

1. Do you know why I have this error on the IMac and not on the Macbook ? g++ -std=gnu++98 -Wall -I. -I. -Isamtools-1.3/htslib-1.3  -O3 -c -o extractRef.o extractRef.cpp

extractRef.cpp:1:17: fatal error: cstdio: No such file or directory

 #include<cstdio>

                 ^

compilation terminated.

make: *** [extractRef.o] Error 1

1. Why the rsem-run-ebseq is not installed although I ran the "make ebseq" command without receiving an error message ?

Thank you,

Jean

[Bo Li]

Hi Jean,

I'm not familiar with Mac OS system.

-Colin, do you have any comments?

For your second question, can you give us the messages when you typed
'make ebseq'?

Thanks,
Bo

On 2016-03-22 09:18, Jean Keller wrote:
> Hi,
>
> I tried to install RSEM on a MacBook Pro with the same version of El
> Capitan and it worked. Howeve, the rsem-run-ebseq command is not
> installed. Consequently, my questions are :
>

> * Do you know why I have this error on the IMac and not on the

> Macbook ? g++ -std=gnu++98 -Wall -I. -I. -Isamtools-1.3/htslib-1.3 
> -O3 -c -o extractRef.o extractRef.cpp
>
> extractRef.cpp:1:17: fatal error: cstdio: No such file or directory
>
>  #include<cstdio>
>
>                  ^
>
> compilation terminated.
>

> make: *** [extractRef.o] Error 1 * Why the rsem-run-ebseq is not

> installed although I ran the "make ebseq" command without receiving an
> error message ?
>
> Thank you,
>
> Jean
>

> *
> *  

>
> Le jeudi 17 mars 2016 22:36:37 UTC+1, Jean Keller a écrit :
>
>> Dear Bo,
>>
>> Thank you for your quick answer.
>> I have the latest version of xcode installed (7.2.1). Recently, I
>> experienced some compilation troubles due to clang Apple compiler.
>> On the last program, I solved the problem by typing "export
>> cc=clang", however it did not work for RSEM.
>>
>> Best,
>>
>> Jean
>

[Jean Keller]

ear Bo,

Thank you for your answer.

Concerning the rem-run-ebseq command, I tried to reinstall Ebzseq on my MacBook and I did not get an error message :

cd EBSeq && /Library/Developer/CommandLineTools/usr/bin/make all

./install

Le chargement a nécessité le package : blockmodeling

Le chargement a nécessité le package : gplots

Attachement du package : ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Le chargement a nécessité le package : testthat

Le chargement a nécessité le package : methods

EBSeq v1.10.0 already exists.

It seems that it is correctly install but there is no rsem-run-ebseq command. 

Best,

Jean

[Bo Li]

Hi Jean,

rsem-run-ebseq is not under EBSeq folder, it is in the main directory.

Hope it helps,
Bo

>>>  RSEM website: http://deweylab.biostat.wisc.edu/rsem/ [1] [1]

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>> it,
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>> [2] [2].
>>>
>>>
>>> Links:
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