no such file or directory: ./pear

[Hannah Vollmer]

Hello, 

Like many others here I am having trouble installing PEAR.  I am working on my MacBook Pro 8, macOS Monterey 12.6.  

I have downloaded and unzipped the files from here: https://www.h-its.org/downloads/pear-academic/

I've tried some different ways, like installing with miniconda in Terminal.  I've also changed the Terminal directory to where the pear-src-0.9.11 folder is and ran './configure && make && make install' with this as output: 

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a race-free mkdir -p... ./install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking whether make sets $(MAKE)... yes

checking whether make supports nested variables... yes

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether the compiler supports GNU C... yes

checking whether gcc accepts -g... yes

checking for gcc option to enable C11 features... none needed

checking whether gcc understands -c and -o together... yes

checking whether make supports the include directive... yes (GNU style)

checking dependency style of gcc... gcc3

checking for log in -lm... yes

checking for main in -lpthread... yes

checking for stdio.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for strings.h... yes

checking for sys/stat.h... yes

checking for sys/types.h... yes

checking for unistd.h... yes

checking for stdint.h... (cached) yes

checking for stdlib.h... (cached) yes

checking for string.h... (cached) yes

checking for inline... inline

checking for size_t... yes

checking for uint32_t... yes

checking build system type... x86_64-apple-darwin21.6.0

checking host system type... x86_64-apple-darwin21.6.0

checking for GNU libc compatible malloc... yes

checking for working strtod... yes

checking for memmove... yes

checking for pow... yes

checking for strtol... yes

checking for library containing pthread_create... none required

checking for library containing BZ2_bzCompress... -lbz2

checking for library containing zlibVersion... -lz

checking for pthread.h... yes

checking for bzlib.h... yes

checking for zlib.h... yes

checking that generated files are newer than configure... done

configure: creating ./config.status

config.status: creating Makefile

config.status: creating src/Makefile

config.status: creating man/Makefile

config.status: creating src/config.h

config.status: src/config.h is unchanged

config.status: executing depfiles commands

Making all in src

/Library/Developer/CommandLineTools/usr/bin/make  all-am

Making all in man

make[1]: Nothing to be done for `all'.

make[1]: Nothing to be done for `all-am'.

Making install in src

 .././install-sh -c -d '/usr/local/bin'

  /usr/bin/install -c pear '/usr/local/bin'

make[2]: Nothing to be done for `install-data-am'.

Making install in man

make[2]: Nothing to be done for `install-exec-am'.

 .././install-sh -c -d '/usr/local/share/man/man1'

 /usr/bin/install -c -m 644 pear.1 '/usr/local/share/man/man1'

make[2]: Nothing to be done for `install-exec-am'.

make[2]: Nothing to be done for `install-data-am'.

It is (apparently) installed, because when I type 'pear' into Terminal it will give me all the pear commands.  However when I try to run: 

./pear f- out.Pool-1_S1_L001_R1_001.fastq.gz -r out.Pool-1_S1_L001_R2_001.fastq.gz -o pool1pear 

I get: 

zsh: no such file or directory: ./pear

I've also asked Terminal 'whereis pear' and got: 

pear: /Users/hannahvollmer/miniconda3/bin/pear /Users/hannahvollmer/miniconda3/share/man/man1/pear.1 

(this second one was something downloaded 2 years ago, not sure what it is)

I tried a fix described in a prior thread that involved installing Rosetta, it is not supported.  (I even downloaded Skype to see if it would prompt me to get Rosetta, it didn't)

I'm new at command line languages and software in general so hopefully the fix is something simple.  Been working on this for days though :/

Hannah

[Alexandros Stamatakis]

just try typing pear instead of ./pear that should work,

Alexis

On 04.05.23 19:17, Hannah Vollmer wrote:
> Hello,
>
> Like many others here I am having trouble installing PEAR.  I am working
> on my MacBook Pro 8, macOS Monterey 12.6.
> I have downloaded and unzipped the files from here:
> https://www.h-its.org/downloads/pear-academic/

> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.h-its.org%2Fdownloads%2Fpear-academic%2F&data=05%7C01%7Chvollmer%40plymouth.edu%7C26e019bfeb3b4da53a6808db4c24faaf%7Cd6241893512d46dc8d2bbe47e25f5666%7C0%7C0%7C638187493921296531%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4ml8NbneBuFy%2BPaf7T87vb0MjR0vWufkSOeiyGsYKqo%3D&reserved=0>

> --
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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Hannah Vollmer]

That just returns the list of commands.  

[Thomas Flouris]

Hi Hannah,

how about running it this way:

/Users/hannahvollmer/miniconda3/bin/pear -f out.Pool-1_S1_L001_R1_001.fastq.gz -r out.Pool-1_S1_L001_R2_001.fastq.gz -o pool1pear

Tomas

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[Hannah Vollmer]

That still just returns the list of commands. 

[Thomas Flouris]

Hi Hannah,

with list of commands you mean the options for PEAR? We first need to make sure you can run the pear executable. If that works, and you're getting the list of PEAR command-line options, then a common problem with MAC users is the dash symbol. I think the '-' symbol does not correspond to the correct ascii character when copying from the web or emails. Try typing the command manually in the console (or at least the dashes) to see if that works.

Tomas

[Hannah Vollmer]

Yes, I mean it was just returning the pear options.

But now it's working!  This was the sweet spot, typed directly into Terminal:

/Users/hannahvollmer/miniconda3/bin/pear -f out.Pool-1_S1_L001_R1_001.fastq.gz -r out.Pool-1_S1_L001_R2_001.fastq.gz -o pool1pear

Hoping I can copy this from Terminal to paste into Stickies like I've been doing so I can modify and copy again when running different pools.  Took me several tries to type it in Terminal without misspelling, lol.