Issue 281: MSStats (Skyline External Tool) installation is noisy and full of scary warnings

issues
Status:open
Assigned To:Brian Pratt
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2014-01-06 by Brian Pratt
Changed:2014-08-28 by Brendan MacLean
Resolved:
Resolution:
Closed:
2014-01-06 Brian Pratt
Title»MSStats (Skyline External Tool) installation is noisy and full of scary warnings
Assigned To»bspratt
Type»Defect
Area»Skyline
Priority»3
Milestone»2.1
This is the outcome of a successful install (64 bit Skyline, SVN 5408) - it gives the impression of trouble, if not outright failure:
----------------------

also installing the dependencies 'bitops', 'gtools', 'gdata', 'caTools'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/bitops_1.0-6.zip'
Content type 'application/zip' length 35878 bytes (35 Kb)
opened URL
downloaded 35 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/gtools_3.1.1.zip'
Content type 'application/zip' length 111097 bytes (108 Kb)
opened URL
downloaded 108 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/gdata_2.13.2.zip'
Content type 'application/zip' length 851188 bytes (831 Kb)
opened URL
downloaded 831 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/caTools_1.16.zip'
Content type 'application/zip' length 227643 bytes (222 Kb)
opened URL
downloaded 222 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/gplots_2.12.1.zip'
Content type 'application/zip' length 474811 bytes (463 Kb)
opened URL
downloaded 463 Kb

package 'bitops' successfully unpacked and MD5 sums checked
package 'gtools' successfully unpacked and MD5 sums checked
package 'gdata' successfully unpacked and MD5 sums checked
package 'caTools' successfully unpacked and MD5 sums checked
package 'gplots' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
also installing the dependencies 'Matrix', 'minqa', 'Rcpp', 'RcppEigen'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/Matrix_1.1-1.1.zip'
Content type 'application/zip' length 3546053 bytes (3.4 Mb)
opened URL
downloaded 3.4 Mb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/minqa_1.2.2.zip'
Content type 'application/zip' length 610224 bytes (595 Kb)
opened URL
downloaded 595 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/Rcpp_0.10.6.zip'
Content type 'application/zip' length 3437621 bytes (3.3 Mb)
opened URL
downloaded 3.3 Mb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/RcppEigen_0.3.2.0.1.zip'
Content type 'application/zip' length 2192710 bytes (2.1 Mb)
opened URL
downloaded 2.1 Mb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/lme4_1.0-5.zip'
Content type 'application/zip' length 3438844 bytes (3.3 Mb)
opened URL
downloaded 3.3 Mb

package 'Matrix' successfully unpacked and MD5 sums checked
package 'minqa' successfully unpacked and MD5 sums checked
package 'Rcpp' successfully unpacked and MD5 sums checked
package 'RcppEigen' successfully unpacked and MD5 sums checked
package 'lme4' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
also installing the dependency 'plyr'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/plyr_1.8.zip'
Content type 'application/zip' length 740147 bytes (722 Kb)
opened URL
downloaded 722 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/reshape_0.8.4.zip'
Content type 'application/zip' length 125652 bytes (122 Kb)
opened URL
downloaded 122 Kb

package 'plyr' successfully unpacked and MD5 sums checked
package 'reshape' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
also installing the dependencies 'colorspace', 'stringr', 'RColorBrewer', 'dichromat', 'munsell', 'labeling', 'digest', 'gtable', 'reshape2', 'scales', 'proto'

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/colorspace_1.2-4.zip'
Content type 'application/zip' length 384429 bytes (375 Kb)
opened URL
downloaded 375 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/stringr_0.6.2.zip'
Content type 'application/zip' length 74936 bytes (73 Kb)
opened URL
downloaded 73 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/RColorBrewer_1.0-5.zip'
Content type 'application/zip' length 25286 bytes (24 Kb)
opened URL
downloaded 24 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/dichromat_2.0-0.zip'
Content type 'application/zip' length 147536 bytes (144 Kb)
opened URL
downloaded 144 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/munsell_0.4.2.zip'
Content type 'application/zip' length 126021 bytes (123 Kb)
opened URL
downloaded 123 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/labeling_0.2.zip'
Content type 'application/zip' length 40403 bytes (39 Kb)
opened URL
downloaded 39 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/digest_0.6.4.zip'
Content type 'application/zip' length 136446 bytes (133 Kb)
opened URL
downloaded 133 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/gtable_0.1.2.zip'
Content type 'application/zip' length 63489 bytes (62 Kb)
opened URL
downloaded 62 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/reshape2_1.2.2.zip'
Content type 'application/zip' length 60508 bytes (59 Kb)
opened URL
downloaded 59 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/scales_0.2.3.zip'
Content type 'application/zip' length 157943 bytes (154 Kb)
opened URL
downloaded 154 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/proto_0.3-10.zip'
Content type 'application/zip' length 458271 bytes (447 Kb)
opened URL
downloaded 447 Kb

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/ggplot2_0.9.3.1.zip'
Content type 'application/zip' length 2657990 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

package 'colorspace' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
package 'dichromat' successfully unpacked and MD5 sums checked
package 'munsell' successfully unpacked and MD5 sums checked
package 'labeling' successfully unpacked and MD5 sums checked
package 'digest' successfully unpacked and MD5 sums checked
package 'gtable' successfully unpacked and MD5 sums checked
package 'reshape2' successfully unpacked and MD5 sums checked
package 'scales' successfully unpacked and MD5 sums checked
package 'proto' successfully unpacked and MD5 sums checked
package 'ggplot2' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
trying URL 'http://www.bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/BiocInstaller_1.12.0.zip'
Content type 'application/zip' length 52475 bytes (51 Kb)
opened URL
downloaded 51 Kb

package 'BiocInstaller' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'limma'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/limma_3.18.7.zip'
Content type 'application/zip' length 1589589 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

package 'limma' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Old packages: 'foreign', 'lattice', 'mgcv', 'nlme', 'rpart'
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'preprocessCore'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/preprocessCore_1.24.0.zip'
Content type 'application/zip' length 203265 bytes (198 Kb)
opened URL
downloaded 198 Kb

package 'preprocessCore' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Old packages: 'foreign', 'lattice', 'mgcv', 'nlme', 'rpart'
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'marray'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/marray_1.40.0.zip'
Content type 'application/zip' length 4475968 bytes (4.3 Mb)
opened URL
downloaded 4.3 Mb

package 'marray' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Old packages: 'foreign', 'lattice', 'mgcv', 'nlme', 'rpart'
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/Rcpp_0.10.6.zip'
Content type 'application/zip' length 3437621 bytes (3.3 Mb)
opened URL
downloaded 3.3 Mb

package 'Rcpp' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'MSnbase'
also installing the dependencies 'affyio', 'zlibbioc', 'BiocGenerics', 'Biobase', 'mzR', 'IRanges', 'vsn', 'affy', 'impute'

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/affyio_1.30.0.zip'
Content type 'application/zip' length 161245 bytes (157 Kb)
opened URL
downloaded 157 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/zlibbioc_1.8.0.zip'
Content type 'application/zip' length 246937 bytes (241 Kb)
opened URL
downloaded 241 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/BiocGenerics_0.8.0.zip'
Content type 'application/zip' length 385432 bytes (376 Kb)
opened URL
downloaded 376 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/Biobase_2.22.0.zip'
Content type 'application/zip' length 2335919 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/mzR_1.8.0.zip'
Content type 'application/zip' length 3231177 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/IRanges_1.20.6.zip'
Content type 'application/zip' length 1971771 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/vsn_3.30.0.zip'
Content type 'application/zip' length 1463860 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/affy_1.40.0.zip'
Content type 'application/zip' length 1462050 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/impute_1.36.0.zip'
Content type 'application/zip' length 669388 bytes (653 Kb)
opened URL
downloaded 653 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/MSnbase_1.10.3.zip'
Content type 'application/zip' length 2384393 bytes (2.3 Mb)
opened URL
downloaded 2.3 Mb

package 'affyio' successfully unpacked and MD5 sums checked
package 'zlibbioc' successfully unpacked and MD5 sums checked
package 'BiocGenerics' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'mzR' successfully unpacked and MD5 sums checked
package 'IRanges' successfully unpacked and MD5 sums checked
package 'vsn' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
package 'impute' successfully unpacked and MD5 sums checked
package 'MSnbase' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f\downloaded_packages
Old packages: 'foreign', 'lattice', 'mgcv', 'nlme', 'rpart'
trying URL 'http://www.stat.purdue.edu/~choi67/MSstats_2.1.3.tar.gz'
Content type 'application/x-tar' length 1909464 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

* installing *source* package 'MSstats' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.10.5)
than is installed on your system (0.10.6). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Warning: replacing previous import by 'ggplot2::fortify' when loading 'MSstats'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.10.5)
than is installed on your system (0.10.6). This might lead to errors
when loading mzR. If you encounter such issues, please send
*** arch - x64
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Warning: replacing previous import by 'ggplot2::fortify' when loading 'MSstats'
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.10.5)
than is installed on your system (0.10.6). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Warning: replacing previous import by 'ggplot2::fortify' when loading 'MSstats'
* DONE (MSstats)
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="C:\Users\bspratt\AppData\Local\Temp\Rtmp80iT9f/MSstats_2.1.3.tar.gz": The system cannot find the file specified

2014-01-08 Brendan MacLean
Milestone2.1»2.6

2014-08-28 Brendan MacLean
Milestone2.6»