Can't find raw files from R script in downloads #17

grace-ac · 2017-10-24T18:19:14Z

I can't find the .raw files that should have been put in the downloads on this computer.

What I could find, was this, and the time stamp matches when I executed the R script:

laurahspencer · 2017-10-24T18:36:44Z

Are you using Woodpecker? I may have moved them to the trash while cleaning up files. Also, FYI I changed the script to download in your current working directory to make it more universa.

…

On Tue, Oct 24, 2017 at 11:20 AM grace-ac ***@***.***> wrote: I can't find the .raw files that should have been put in the downloads on this computer. What I could find, was this, and the time stamp matches when I executed the R script: [image: capture] <https://user-images.githubusercontent.com/14934314/31960564-0c2c7de6-b8ad-11e7-8d19-f697fa0daf4d.PNG> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQdwfSm-twfk2rlqR8Rr94oBCEG_oEEFks5svioigaJpZM4QE33f> .

grace-ac · 2017-10-24T19:03:03Z

Ah, ok. I'm using the one in 228 (Swan). I'll check the working directory.

grace-ac · 2017-10-24T20:30:08Z

This is all I can seem to find:

It matches the name that the RScript says it will be called:

sr320 · 2017-10-24T21:31:24Z

Here is a screen cast showing the problems in the Step 1 of
https://github.com/RobertsLab/Paper-DNR-Geoduck-Proteomics/blob/master/notebooks/SRM/00-Download-raw-data.md

http://d.pr/v/sXPWZy

Seems like forward slashes are problem? and nothing downloads

(at least you can see my logic if it is faulty)

laurahspencer · 2017-10-24T23:35:56Z

I updated the first couple lines of the script, removing the first /

 dir.create("2017-Geoduck-SRM-raw/")   
 setwd("2017-Geoduck-SRM-raw/")

This revised script worked on Woodpecker, so hopefully @grace-ac it will work for you too?

sr320 · 2017-10-24T23:49:00Z

It will likely not..... see my screencast

That is a needed correction but the next block fails....

kubu4 · 2017-10-25T00:50:34Z

Downloads fail on Ubuntu (related to package installs; never actually get to attempting downloads). Error messages are listed below (too long for screen caps). This is on R 3.2.3.

Provides more support that all of this should be contained in a Gti repo. Someone downloads entire repo and has all the files. R script then uses relative paths to files within that repo.

installing source package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:

deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
rpm: libcurl-devel (Fedora, CentOS, RHEL)
csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘curl’

removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
installing source package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
deb: libssl-dev (Debian, Ubuntu, etc)
rpm: openssl-devel (Fedora, CentOS, RHEL)
csw: libssl_dev (Solaris)
brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘openssl’

removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
installing source package ‘praise’ ...
** package ‘praise’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
DONE (praise)
installing source package ‘rex’ ...
** package ‘rex’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
DONE (rex)
installing source package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
DONE (stringr)
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status
installing source package ‘testthat’ ...
** package ‘testthat’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c label.c -o label.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reassign.c -o reassign.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-catch.cpp -o test-catch.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-example.cpp -o test-example.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-runner.cpp -o test-runner.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib/R/lib -lR
installing to /home/samb/R/x86_64-pc-linux-gnu-library/3.2/testthat/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
DONE (testthat)
ERROR: dependency ‘httr’ is not available for package ‘covr’
removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/covr’
Warning in install.packages :
installation of package ‘covr’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpUhCsyJ/downloaded_packages’

install.packages("curl", dep=TRUE)
Installing package into ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependency ‘webutils’

--2017-10-24 17:38:45-- https://cran.rstudio.com/src/contrib/webutils_0.6.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 13.32.207.112
Connecting to cran.rstudio.com (cran.rstudio.com)|13.32.207.112|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 22694 (22K) [application/x-gzip]
Saving to: ‘/tmp/RtmpUhCsyJ/downloaded_packages/webutils_0.6.tar.gz’

 0K .......... .......... ..                              100%  342M=0s

2017-10-24 17:38:45 (342 MB/s) - ‘/tmp/RtmpUhCsyJ/downloaded_packages/webutils_0.6.tar.gz’ saved [22694/22694]

--2017-10-24 17:38:45-- https://cran.rstudio.com/src/contrib/curl_3.0.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 13.32.207.112
Connecting to cran.rstudio.com (cran.rstudio.com)|13.32.207.112|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 412212 (403K) [application/x-gzip]
Saving to: ‘/tmp/RtmpUhCsyJ/downloaded_packages/curl_3.0.tar.gz’

 0K .......... .......... .......... .......... .......... 12% 7.25M 0s
50K .......... .......... .......... .......... .......... 24% 8.07M 0s

100K .......... .......... .......... .......... .......... 37% 12.1M 0s
150K .......... .......... .......... .......... .......... 49% 7.33M 0s
200K .......... .......... .......... .......... .......... 62% 12.0M 0s
250K .......... .......... .......... .......... .......... 74% 7.54M 0s
300K .......... .......... .......... .......... .......... 86% 6.02M 0s
350K .......... .......... .......... .......... .......... 99% 10.0M 0s
400K .. 100% 4865G=0.05s

2017-10-24 17:38:45 (8.36 MB/s) - ‘/tmp/RtmpUhCsyJ/downloaded_packages/curl_3.0.tar.gz’ saved [412212/412212]

installing source package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
rpm: libcurl-devel (Fedora, CentOS, RHEL)
csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘curl’

removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
ERROR: dependency ‘curl’ is not available for package ‘webutils’
removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/webutils’
Warning in install.packages :
installation of package ‘webutils’ had non-zero exit statu

laurahspencer · 2017-10-25T02:45:10Z

@sr320 can you try running the entire script now that I've made the edit to the first few lines? In your screencast you did not run the whole script, which is required to actually download the files. Most of the lines in this script create objects in R, to be used by R, to download the correct urls and save with the correct names.

@kubu4 does the script work in RStudio using Ubuntu?

kubu4 · 2017-10-25T03:08:57Z

No - it fails on installing cURL. Although, it proceeds through the script and spits out "FALSE" (because it couldn't install cURL).

See my comment above.

grace-ac · 2017-10-25T21:54:48Z

Just used the new script in the notebook and it worked!

grace-ac added question SRM-protocol labels Oct 24, 2017

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Can't find raw files from R script in downloads #17

Can't find raw files from R script in downloads #17

grace-ac commented Oct 24, 2017

laurahspencer commented Oct 24, 2017 via email

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grace-ac commented Oct 25, 2017

Can't find raw files from R script in downloads #17

Can't find raw files from R script in downloads #17

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