I'm using bash_completion in order to hit tab and see branch names and directories. That all works. I placed this into my bash_profile in order to connect bash_completion:
if [ -f `brew --prefix`/etc/bash_completion ]; then
. `brew --prefix`/etc/bash_completion
fi
When I start my terminal now I get:
-bash: #MyNameHERE: command not found
If I remove the first snippet from the bash_profile, this goes away, but then bash_completion doesn't work. Any thoughts?
Brew Doctor results:
Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry and just ignore them. Thanks!
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/node/android-ifaddrs.h
/usr/local/include/node/ares.h
/usr/local/include/node/ares_version.h
/usr/local/include/node/libplatform/libplatform.h
/usr/local/include/node/nameser.h
/usr/local/include/node/node.h
/usr/local/include/node/node_buffer.h
/usr/local/include/node/node_internals.h
/usr/local/include/node/node_object_wrap.h
/usr/local/include/node/node_version.h
/usr/local/include/node/openssl/aes.h
/usr/local/include/node/openssl/archs/aix-gcc/opensslconf.h
/usr/local/include/node/openssl/archs/aix64-gcc/opensslconf.h
/usr/local/include/node/openssl/archs/BSD-x86/opensslconf.h
/usr/local/include/node/openssl/archs/BSD-x86_64/opensslconf.h
/usr/local/include/node/openssl/archs/darwin-i386-cc/opensslconf.h
/usr/local/include/node/openssl/archs/darwin64-x86_64-cc/opensslconf.h
/usr/local/include/node/openssl/archs/linux-aarch64/opensslconf.h
/usr/local/include/node/openssl/archs/linux-armv4/opensslconf.h
/usr/local/include/node/openssl/archs/linux-elf/opensslconf.h
/usr/local/include/node/openssl/archs/linux-ppc/opensslconf.h
/usr/local/include/node/openssl/archs/linux-ppc64/opensslconf.h
/usr/local/include/node/openssl/archs/linux-x32/opensslconf.h
/usr/local/include/node/openssl/archs/linux-x86_64/opensslconf.h
/usr/local/include/node/openssl/archs/solaris-x86-gcc/opensslconf.h
/usr/local/include/node/openssl/archs/solaris64-x86_64-gcc/opensslconf.h
/usr/local/include/node/openssl/archs/VC-WIN32/opensslconf.h
/usr/local/include/node/openssl/archs/VC-WIN64A/opensslconf.h
/usr/local/include/node/openssl/asn1.h
/usr/local/include/node/openssl/asn1_mac.h
/usr/local/include/node/openssl/asn1t.h
/usr/local/include/node/openssl/bio.h
/usr/local/include/node/openssl/blowfish.h
/usr/local/include/node/openssl/bn.h
/usr/local/include/node/openssl/buffer.h
/usr/local/include/node/openssl/camellia.h
/usr/local/include/node/openssl/cast.h
/usr/local/include/node/openssl/cmac.h
/usr/local/include/node/openssl/cms.h
/usr/local/include/node/openssl/comp.h
/usr/local/include/node/openssl/conf.h
/usr/local/include/node/openssl/conf_api.h
/usr/local/include/node/openssl/crypto.h
/usr/local/include/node/openssl/des.h
/usr/local/include/node/openssl/des_old.h
/usr/local/include/node/openssl/dh.h
/usr/local/include/node/openssl/dsa.h
/usr/local/include/node/openssl/dso.h
/usr/local/include/node/openssl/dtls1.h
/usr/local/include/node/openssl/e_os2.h
/usr/local/include/node/openssl/ebcdic.h
/usr/local/include/node/openssl/ec.h
/usr/local/include/node/openssl/ecdh.h
/usr/local/include/node/openssl/ecdsa.h
/usr/local/include/node/openssl/engine.h
/usr/local/include/node/openssl/err.h
/usr/local/include/node/openssl/evp.h
/usr/local/include/node/openssl/hmac.h
/usr/local/include/node/openssl/idea.h
/usr/local/include/node/openssl/krb5_asn.h
/usr/local/include/node/openssl/kssl.h
/usr/local/include/node/openssl/lhash.h
/usr/local/include/node/openssl/md4.h
/usr/local/include/node/openssl/md5.h
/usr/local/include/node/openssl/mdc2.h
/usr/local/include/node/openssl/modes.h
/usr/local/include/node/openssl/obj_mac.h
/usr/local/include/node/openssl/objects.h
/usr/local/include/node/openssl/ocsp.h
/usr/local/include/node/openssl/opensslconf.h
/usr/local/include/node/openssl/opensslv.h
/usr/local/include/node/openssl/ossl_typ.h
/usr/local/include/node/openssl/pem.h
/usr/local/include/node/openssl/pem2.h
/usr/local/include/node/openssl/pkcs12.h
/usr/local/include/node/openssl/pkcs7.h
/usr/local/include/node/openssl/pqueue.h
/usr/local/include/node/openssl/rand.h
/usr/local/include/node/openssl/rc2.h
/usr/local/include/node/openssl/rc4.h
/usr/local/include/node/openssl/ripemd.h
/usr/local/include/node/openssl/rsa.h
/usr/local/include/node/openssl/safestack.h
/usr/local/include/node/openssl/seed.h
/usr/local/include/node/openssl/sha.h
/usr/local/include/node/openssl/srp.h
/usr/local/include/node/openssl/srtp.h
/usr/local/include/node/openssl/ssl.h
/usr/local/include/node/openssl/ssl2.h
/usr/local/include/node/openssl/ssl23.h
/usr/local/include/node/openssl/ssl3.h
/usr/local/include/node/openssl/stack.h
/usr/local/include/node/openssl/symhacks.h
/usr/local/include/node/openssl/tls1.h
/usr/local/include/node/openssl/ts.h
/usr/local/include/node/openssl/txt_db.h
/usr/local/include/node/openssl/ui.h
/usr/local/include/node/openssl/ui_compat.h
/usr/local/include/node/openssl/whrlpool.h
/usr/local/include/node/openssl/x509.h
/usr/local/include/node/openssl/x509_vfy.h
/usr/local/include/node/openssl/x509v3.h
/usr/local/include/node/pthread-fixes.h
/usr/local/include/node/stdint-msvc2008.h
/usr/local/include/node/tree.h
/usr/local/include/node/uv-aix.h
/usr/local/include/node/uv-bsd.h
/usr/local/include/node/uv-darwin.h
/usr/local/include/node/uv-errno.h
/usr/local/include/node/uv-linux.h
/usr/local/include/node/uv-sunos.h
/usr/local/include/node/uv-threadpool.h
/usr/local/include/node/uv-unix.h
/usr/local/include/node/uv-version.h
/usr/local/include/node/uv-win.h
/usr/local/include/node/uv.h
/usr/local/include/node/v8-debug.h
/usr/local/include/node/v8-platform.h
/usr/local/include/node/v8-profiler.h
/usr/local/include/node/v8-testing.h
/usr/local/include/node/v8-util.h
/usr/local/include/node/v8-version.h
/usr/local/include/node/v8.h
/usr/local/include/node/v8config.h
/usr/local/include/node/zconf.h
/usr/local/include/node/zlib.h
Set -xv Results:
https://raw.githubusercontent.com/SpencerRohan/debug/master/README.md
This:
-bash: #MyNameHERE: command not found
is telling you it is trying to execute the command #MyNameHERE
and it doesn't find it in your system.
Try replacing:
if [ -f `brew --prefix`/etc/bash_completion ]; then
. `brew --prefix`/etc/bash_completion
fi
with
brewPrefix=`brew --prefix`
if [ -f "${brewPrefix}/etc/bash_completion" ]; then
. "${brewPrefix}/etc/bash_completion"
fi
my wild guess is that some space in the return value of brew --prefix can cause this
if this still doesn't work try setting the full path in the brewPrefix variable (comment the other line with a #). the execution in .bash_profile sometimes do not work like executing it in your usual terminal because environment variables are different
Also make sure that snippet is placed at the BOTTOM of the .bash_profile
Related
featureCounts was called under minconda in Linux subsystem on a Windows 10 computer.
featureCounts -a /mnt/d/.../__.txt -F SAF -readExtensions3 200 -o ___.tsv -O file1.bam file2.bam file3p.bam file4.bam file5.bam file6.bam file7.bam file8.bam
This always results in an error message
featureCounts: invalid option -- 'r'
Version 2.0.1
Usage: featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ...
## Mandatory arguments:
-a <string> Name of an annotation file. GTF/GFF format by default. See...
And then reprinting the required and optional arguments for featureCounts function.
Does anyone know what does the error message "invalid option --'r'" mean? And how can I fix it?
Is there any difference between calling featureCounts in command prompt (or Terminal on Mac) and calling it in Linux/miniconda3?
It seems that you mistyped option name, it should be --readExtension3 with two dashes in front of it and without 's' in the end. I had a similar problem with --fraction which led me here!
i am not root user,so i install aria2-1.34.0 with ./configure --prefix=/home/xxx/.local, everything works fine but on-download-complete
i set on-download-complete=/home/xxx/aria2/a.sh
#!/bin/bash
echo 123 > 1.txt
when a task download completed, the log shows everything is ok
2019-10-28 19:04:11.295587 [NOTICE] [RequestGroup.cc:1216] Download complete: /home/xxx/aria2/data/0.png
2019-10-28 19:04:11.295598 [INFO] [DefaultBtProgressInfoFile.cc:415] The segment file /home/xxx/aria2/data/0.png.aria2 does not exist.
2019-10-28 19:04:11.295612 [INFO] [util.cc:2239] Executing user command: /home/xxx/aria2/a.sh b031d9399fb9d93f 1 /home/xxx/aria2/data/0.png
but actually nothing happened, it didn't work!!!
aria2c path:
/home/xxx/.local/aria2c
aria2.conf
enable-rpc=true
rpc-allow-origin-all=true
rpc-listen-all=false
max-concurrent-downloads=1
continue=true
max-connection-per-server=5
min-split-size=5M
split=5
max-overall-download-limit=5M
max-download-limit=2M
max-overall-upload-limit=0
max-upload-limit=0
dir=/home/xxx/aria2/data
file-allocation=prealloc
on-download-complete=/home/xxx/aria2/a.sh
log=/home/xxx/aria2/aria2.log
log-level=info
i don't know how to deal with it, could u give me any suggestions, thanks.
got a solution for me
put --on-download-complete in cmd instead of aria2.conf
just run aria2 like:
aria2c --conf-path=/xxx/xxx/arai2.conf --on-download-complete=/xxx/xxx/xxx.sh -D
and it works
but i have no idea why it didn't work if set --on-download-complete in conf file
Accroding to the official document
-D, --daemon [true|false]
Run as daemon. The current working directory will be changed to / and standard input, standard output and standard error will be redirected to /dev/null. Default: false
You should modify /home/xxx/aria2/a.sh to
#!/bin/bash
echo 123 > $(dirname $0)/1.txt
to write the output to the right place.
I have been using a script launching GMT (General Mapping Tool) commandlines from a directory for a while. But now, the GMT commandline is not working in this directory anymore. It just enters and does not output anything, even informations on the version of the commandline.
/media/data/user/weird_directory/child_directory
This weird behavior is only located in the script directory though (weird_directory), and the commandline is working in the child (child_directory) and parent directories (user). I can thus launch my script only from those parent and child directories.
Do you have any idea what I did? What can I do to undo it?
The commandline which gives me problem is:
gmt --version
My path is:
/usr/local/src/SW/BIN/bin:/usr/lib64/qt-3.3/bin:/usr/local/src/SW/QT5/5.1.1/5.1.1/gcc_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/data/STUD/aargentin/bin
My .bashrc only has inside:
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
Here is my directory content when I use ls -a:
0
0]
.
..
1000705
1000799
1000849
1000858
1000151
1000507
1001158
1001333
1001343
1001563
1001669
1001741
1001777
1001805
1001834
1002029
1002087
1002125
100216
1002282
1002310
1002387
1002647
1002678
1002700
100273
100319
100325
1003326
10036
1003615
1003842
1004278
1004362
1004398
1004884
1004974
1005068
1005082
1005205
1005411
1005791
1005832
1005873
1006295
1006696
100682
100706
1007061
1007533
1007635
1007766
1007871
cut_DEMgrd.grd
cut_only_rockfalls_DEM.grd
cut_rockfallgrd.grd
cut_without_rockfalls_DEM.grd
DEMgrd.grd
dhm_at_lamb_10m_2018_part1_depressionless.tif
dhm_at_lamb_10m_2018_part1_depressionless.tif.aux.xml
gmt.conf
gmt.history
kdtpTC3JJ
only_rockfalls_DEM.grd
rockfallgrd.grd
subtract_rockfall_to_flt_DEM.sh
subtract_rockfall_to_flt_DEM.sh~
without_rockfalls_DEM.grd
gmt.history is empty and gmt.conf only contains a printing option:
#
# GMT 5.4.2 Defaults file
#
# PostScript Parameters
#
PS_MEDIA = a2
For future reference, I tried deleting the gmt.history file that was empty, and the gmt command now works again.
I'm trying to install Orbfit4.2 on a using linux mint maya edition. I'm trying to follow the on line help. I have unzipped the tared file, configured with $ ./config -0 gfortran and then $ make. Both appears to be successful. I am now trying to create the DE405 data files in the /orbfit/src/jpleph directory. I have downloaded the header.405 and the ascp*date* ascii files into the directory from JPL. I have run $ make ephemerides and get the following;
cat header.405 ascp1960.405 ascp1980.405 ascp2000.405 ascp2020.405> input.430
asc2eph.x < input.430
/bin/sh: 1: asc2eph.x: not found
make: *** [ephemerides] Error 127
(I have also used input value of 405 instead of 430)
I have also tried just running from with in
the directory
$ ./asc2eph.x which was the previous method before the Makefile was included. All I get with this is 'authors' introductory message and the flashing working box-still running 6 hrs later.
If anybody has any experience or advice with installing Orbfit 4.2 from the start or can help me move on from the above blockage I would appreciate.
Note I am a real novice and would appreciate idiot step by step guide- I'm the idiot.
Eric
The Makefile assumes that the current directory "." is in your path. This is a security risk. You can either edit the Makefile to rename these binaries:
$ diff -u Makefile.orig Makefile
--- Makefile.orig 2014-01-09 07:14:10.000000000 -0800
+++ Makefile 2014-10-21 11:40:00.850236839 -0700
## -10,7 +10,7 ##
make clean
ephemerides: input asc2eph.x
- asc2eph.x < input.430
+ ./asc2eph.x < input.430
mv JPLEPH jpleph
make clean
Or you can add . to your path (but this is insecure!) by doing
$ PATH=.:$PATH
update: the error only occurs when logged into R from within emacs
what works:
When I ssh into a remote server and run
$ ./foo.rb
from the bash shell, it works. Furthermore, if I launch R and execute
$ R
system('./foo.rb')
I am in a group with permission to read/write/execute the file. File permissions are -rwxrwx---
what doesn't work:
Launch emacs and start an R session:
M-x R
ssh-myserver:.
system('./foo.rb')
I get the following error:
ruby: Permission denied -- foo.rb (LoadError)
why is this? Is there a way to work around this?
I can not find any information from ?system or ?system2
Here is the output from sessionInfo()
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] PECAn_0.1.1 xtable_1.5-6 gridExtra_0.7 RMySQL_0.7-5
[5] DBI_0.2-5 ggplot2_0.8.9 proto_0.3-8 reshape_0.8.3
[9] plyr_1.6 rjags_2.2.0-2 coda_0.13-5 lattice_0.19-17
[13] randtoolbox_1.09 rngWELL_0.9 MASS_7.3-11 XML_3.2-0
loaded via a namespace (and not attached):
[1] digest_0.4.2
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
output of 'id' and 'env' from ssh and emacs, per comment by #sarnold (changed user names, group names, and ip addresses)
1. server
1.1 'id'
uid=1668(dleb) gid=1668(dleb) groups=117(ebusers),159(lab_admin),166(lab),1340(pal_web),1668(dleb)
1.2 'env'
LC_PAPER=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
SHELL=/usr/local/bin/system-specific
KDE_NO_IPV6=1
SSH_CLIENT=888.888.888.88 51857 22
NCARG_FONTCAPS=/usr/lib64/ncarg/fontcaps
LC_NUMERIC=en_US.UTF-8
USER=dleb
LS_COLORS=
LC_TELEPHONE=en_US.UTF-8
KDEDIR=/usr
NCARG_GRAPHCAPS=/usr/lib64/ncarg/graphcaps
MAIL=/var/mail/dleb
PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin
LC_IDENTIFICATION=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
R_LIBS=/home/a-m/dleb/lib/R
PWD=/home/dleb
NCARG_ROOT=/usr
KDE_IS_PRELINKED=1
LANG=en_US.UTF-8
NCARG_DATABASE=/usr/lib64/ncarg/database
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
LOADEDMODULES=
LC_MEASUREMENT=en_US.UTF-8
NCARG_LIB=/usr/lib64/ncarg
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
NCARG_NCARG=/usr/share/ncarg
SHLVL=1
HOME=/home/a-m/dleb
LOGNAME=dleb
CVS_RSH=ssh
SSH_CONNECTION=888.888.888.88 51857 999.999.999.99 22
LC_CTYPE=en_US.UTF-8
MODULESHOME=/usr/share/Modules
LESSOPEN=|/usr/bin/lesspipe.sh %s
DISPLAY=localhost:15.0
LC_TIME=en_US.UTF-8
G_BROKEN_FILENAMES=1
LC_NAME=en_US.UTF-8
_=/bin/env
emacs/ess R session
2.1 system('id')
uid=1668(dleb) gid=1668(dleb) groups=117(ebusers),159(lab_admin),166(lab),1340(pal_web),1668(dleb)
2.2 system('env')
LN_S=ln -s
R_TEXI2DVICMD=/usr/bin/texi2dvi
LC_PAPER=en_US.UTF-8
SED=/bin/sed
LC_ADDRESS=en_US.UTF-8
R_PDFVIEWER=/usr/bin/xdg-open
LC_MONETARY=en_US.UTF-8
HOSTNAME=ebi-forecast
R_INCLUDE_DIR=/usr/include/R
R_PRINTCMD=lpr
SHELL=/usr/local/bin/system-specific
TERM=dumb
AWK=gawk
HISTSIZE=1
R_RD4DVI=ae
SSH_CLIENT=888.888.888.88 51159 22
KDE_NO_IPV6=1
R_RD4PDF=times,hyper
R_PAPERSIZE=a4
NCARG_FONTCAPS=/usr/lib64/ncarg/fontcaps
PERL=/usr/bin/perl
LC_NUMERIC=en_US.UTF-8
SSH_TTY=/dev/pts/14
LC_ALL=C
EMACS=t
USER=dleb
LC_TELEPHONE=en_US.UTF-8
LS_COLORS=
LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib
TAR=/bin/gtar
ENV=
R_ZIPCMD=/usr/bin/zip
KDEDIR=/usr
PAGER=/usr/bin/less
NCARG_GRAPHCAPS=/usr/lib64/ncarg/graphcaps
R_GZIPCMD=/usr/bin/gzip
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
LC_COLLATE=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
EGREP=/bin/grep -E
PWD=/home/a-m/dleb/pecan
INPUTRC=/etc/inputrc
R_LIBS=/home/a-m/dleb/lib/R
NCARG_ROOT=/usr
R_SHARE_DIR=/usr/share/R
WHICH=/usr/bin/which
EDITOR=vi
LANG=en_US.UTF-8
KDE_IS_PRELINKED=1
R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library
M ODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
NCARG_DATABASE=/usr/lib64/ncarg/database
LC_MEASUREMENT=en_US.UTF-8
LOADEDMODULES=
PS3=
R_BROWSER=/usr/bin/xdg-open
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
NCARG_LIB=/usr/lib64/ncarg
HOME=/home/a-m/dleb
SHLVL=1
NCARG_NCARG=/usr/share/ncarg
R_ARCH=
TR=/usr/bin/tr
MAKE=make
R_UNZIPCMD=/usr/bin/unzip
LOGNAME=dleb
CVS_RSH=ssh
LC_CTYPE=en_US.UTF-8
SSH_CONNECTION=888.888.888.88 51159 999.999.999.99 22
R_BZIPCMD=/usr/bin/bzip2
MODULESHOME=/usr/share/Modules
LESSOPEN=|/usr/bin/lesspipe.sh %s
PROMPT_COMMAND=
R_HOME=/usr/lib64/R
DISPLAY=localhost:22.0
R_PLATFORM=x86_64-redhat-linux-gnu
INSIDE_EMACS=23.2.1,tramp:2.1.18-23.2
R_LIBS_USER=~/R/x86_64-redhat-linux-gnu-library/2.12
LC_TIME=en_US.UTF-8
R_DOC_DIR=/usr/share/doc/R-2.12.2
R_SESSION_TMPDIR=/tmp/RtmpqA6bpJ
HISTFILE=/home/a-m/dleb/.tramp_history
G_BROKEN_FILENAMES=1
LC_NAME=en_US.UTF-8
_=/bin/env
Assuming you started up R as the same user, you do. You error is not coming from a permissions problem for foo.rb, however, or else your shell would be giving the error. (i.e. sh: ./test.rb: Permission denied; see example below). Here, ruby itself is giving the error. Without knowing exactly what is in your foo.rb, I would suggest digging in there to see what it is trying to load/source, and checking the permissions on those.
#!/usr/bin/env ruby
puts 'Hello world'
Now in R....
> system('ls -l test.rb')
-rw-r--r-- 1 jcolby staff 40 Oct 21 08:23 test.rb
> system('./test.rb')
sh: ./test.rb: Permission denied
> system('chmod a+x test.rb')
> system('./test.rb')
Hello world
I presume the M ODULEPATH in the Emacs-derived output is simply a copy and paste typo.
The differences between the two env outputs is much greater than I expected; I've selected the ones that look slightly suspicious to me:
$ diff -u works fails
--- works 2011-10-24 15:04:02.000000000 -0700
+++ fails 2011-10-24 15:12:36.000000000 -0700
...
+LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib
...
-PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin
-PWD=/home/dleb
...
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
...
+PWD=/home/a-m/dleb/pecan
...
In the emacs-derived session, your LD_LIBRARY_PATH environment variable may be changing specifics of which dynamically linked libraries are being used when executing ruby. If you ssh in to your server and execute your foo.rb with the changed LD_LIBRARY_PATH, does it work or fail?
LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib ./foo.rb
The PATH environment variable between the two sessions is different; perhaps you have permission to execute /usr/local/bin/ruby (or the libraries in /usr/local/lib/ruby/) but not /usr/bin/ruby (or the libraries in /usr/lib/ruby/). Does your script use #!env ruby or does it use #!/usr/bin/ruby (or some other fixed path)?
Your pwd in one instance is /home/dleb, the other /home/a-m/dleb/pecan -- but HOME is set to /home/a-m/dleb on both systems. Is /home/dleb a symbolic link or does it actually exist separate from /home/a-m/dleb? (This really is grasping at straws -- I don't think this is it, but this problem is baffling.)
One last thing to consider: is your server confined with a tool such as AppArmor, SELinux, TOMOYO, or SMACK? Any of these mandatory access control tools can prevent an application from writing in specific locations, perhaps they aren't yet configured for your site. Check dmesg(1) output to see if there are any rejection messages, most or all these tools log to dmesg(1) if auditd(8) isn't running.