MSstats(3.5.1) installation error

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cxt...@gmail.com

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Jun 28, 2016, 5:04:07 AM6/28/16
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Hi
   I have met a problem when installing MSstats(3.5.1). It still reminds me an unknown error installing packages, although I have reinstalled skyline(64-bit,3.5.1).

   Could someone give me some suggestion? the details is in slides.

Thanks

MSstats error.pptx

nic...@proteinms.net

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Jun 28, 2016, 6:38:41 AM6/28/16
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The error that you are seeing is (in the Immediate Window in Skyline towards the bottom of your screenshot):
InternetOpenUrl failed: 'The operation timed out'

Usually an error like that is temporary and caused by network connectivity problems. It is likely that if you tried this again it would be successful.

If this problem continues to happen for you, it might be helpful if we could see all of the text in the Immediate Window in Skyline.
Can you select all of that text and paste it into this message?

cxt...@gmail.com

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Jun 28, 2016, 8:35:52 AM6/28/16
to MSstats

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/gplots_3.0.1.zip'
Content type 'application/zip' length 511576 bytes (499 KB)
==================================================
downloaded 499 KB

package 'gplots' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/lme4_1.1-12.zip'
Content type 'application/zip' length 4737751 bytes (4.5 MB)
==================================================
downloaded 4.5 MB

package 'lme4' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/reshape_0.8.5.zip'
Content type 'application/zip' length 126806 bytes (123 KB)
==================================================
downloaded 123 KB

package 'reshape' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/reshape2_1.4.1.zip'
Content type 'application/zip' length 498665 bytes (486 KB)
==================================================
downloaded 486 KB

package 'reshape2' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
Warning messages:
1: package 'grid' is not available (for R version 3.2.4)
2: package 'grid' is a base package, and should not be updated
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/ggplot2_2.1.0.zip'
Content type 'application/zip' length 2002768 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

package 'ggplot2' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/ggrepel_0.5.zip'
Content type 'application/zip' length 1594067 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

package 'ggrepel' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/minpack.lm_1.2-0.zip'
Content type 'application/zip' length 101387 bytes (99 KB)
==================================================
downloaded 99 KB

package 'minpack.lm' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/data.table_1.9.6.zip'
Content type 'application/zip' length 1883630 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

package 'data.table' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpkdJ5md\downloaded_packages
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :


  InternetOpenUrl failed: 'The operation timed out'

Execution halted


 

nic...@proteinms.net

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Jun 28, 2016, 9:30:49 AM6/28/16
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It looks like the MSstats "install packages" script is failing on this line of R code:

Do you have any trouble navigating to the page:
in your web browser?

cxt...@gmail.com

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Jul 3, 2016, 9:54:34 AM7/3/16
to MSstats
I can't.

cxt...@gmail.com

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Jul 3, 2016, 11:38:24 AM7/3/16
to MSstats
Now I can navigate to the page until I have changed the browser, but I still can't install it.

cxt...@gmail.com

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Jul 3, 2016, 12:01:45 PM7/3/16
to MSstats
immediate window says

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/gplots_3.0.1.zip'
Content type 'application/zip' length 511792 bytes (499 KB)
==================================================
downloaded 499 KB
package 'gplots' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/lme4_1.1-12.zip'
Content type 'application/zip' length 4737722 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
package 'lme4' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/reshape_0.8.5.zip'
Content type 'application/zip' length 127360 bytes (124 KB)
==================================================
downloaded 124 KB
package 'reshape' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/reshape2_1.4.1.zip'
Content type 'application/zip' length 498630 bytes (486 KB)
==================================================
downloaded 486 KB
package 'reshape2' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
Warning messages:
1: package 'grid' is not available (for R version 3.2.4)
2: package 'grid' is a base package, and should not be updated
Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/ggplot2_2.1.0.zip'
Content type 'application/zip' length 2002061 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
package 'ggplot2' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/ggrepel_0.5.zip'
Content type 'application/zip' length 1594081 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
package 'ggrepel' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/minpack.lm_1.2-0.zip'
Content type 'application/zip' length 101376 bytes (99 KB)
==================================================
downloaded 99 KB
package 'minpack.lm' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages

Installing package into 'C:/Users/proteome/Documents/R/win-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.2/data.table_1.9.6.zip'
Content type 'application/zip' length 1883494 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
package 'data.table' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
 C:\Users\proteome\AppData\Local\Temp\RtmpmyhP5g\downloaded_packages
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