search

rprops / Phenoflow_package

R package offering functionality for the advanced analysis of microbial flow cytometry data
GNU General Public License v2.0
9 stars 5 forks source link

Clean install on win10, R 3.3.3 does not work ==> dependency settings? #28

Closed FMKerckhof closed 7 years ago

FMKerckhof commented 7 years ago

Issue lies with flowFDA, flowCore or matrixStats:

* installing *source* package 'flowFDA' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'matrixStats'
Error : package 'flowCore' could not be loaded
ERROR: lazy loading failed for package 'flowFDA'
* removing 'C:/Users/fpkerckh/Documents/R/win-library/3.3/flowFDA'

Upon installing flowCore, also flowViz needs to be installed still:

* installing *source* package 'flowFDA' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'IDPmisc'
Error : package 'flowViz' could not be loaded
ERROR: lazy loading failed for package 'flowFDA'
* removing 'C:/Users/fpkerckh/Documents/R/win-library/3.3/flowFDA'

Then, an issue with multcomp appears to be present:

* installing *source* package 'flowFDA' ...
** R
** inst
** preparing package for lazy loading
Error : package 'TH.data' required by 'multcomp' could not be found
ERROR: lazy loading failed for package 'flowFDA'
* removing 'C:/Users/fpkerckh/Documents/R/win-library/3.3/flowFDA'

Which appears to clear the issue. So, only upon manual installation of: flowViz, flowCore and multcomp, Phenoflow could be installed.

FMKerckhof commented 7 years ago

Final sessionInfo():

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252    LC_MONETARY=Dutch_Belgium.1252
[4] LC_NUMERIC=C                   LC_TIME=Dutch_Belgium.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multcomp_1.4-6       TH.data_1.0-8        MASS_7.3-45          survival_2.41-2      mvtnorm_1.0-6       
[6] flowCore_1.40.6      BiocInstaller_1.24.0 devtools_1.12.0
rprops commented 7 years ago

I'll take a look. Similar problem occurred on Centos, issue was with the flowCore/flowViz packages themselves.

rprops commented 7 years ago

@FMKerckhof Can you check if this is still an issue with the latest commit?

FMKerckhof commented 7 years ago

I will give it a go

FMKerckhof commented 7 years ago

On Win7 fresh R install, bioconductor appears to not be installable from scratch:

install_github("rprops/Phenoflow_package")
Downloading GitHub repo rprops/Phenoflow_package@master
from URL https://api.github.com/repos/rprops/Phenoflow_package/zipball/master
Installing Phenoflow
‘BiocInstaller’ must be installed for this functionality.
Would you like to install it?

1: Yes
2: No

Selection: 1
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
In addition: Warning message:
package ‘BiocInstaller’ is not available (for R version 3.3.3)

Output of sessionInfo() is given below:

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252    LC_MONETARY=Dutch_Belgium.1252
[4] LC_NUMERIC=C                   LC_TIME=Dutch_Belgium.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_1.12.0

loaded via a namespace (and not attached):
[1] httr_1.2.1    R6_2.2.0      tools_3.3.3   withr_1.0.2   curl_2.4      memoise_1.0.0 git2r_0.18.0  digest_0.6.12
FMKerckhof commented 7 years ago

Upon installing Bioconductor, the following output is returned:

> install_github("rprops/Phenoflow_package")
Downloading GitHub repo rprops/Phenoflow_package@master
from URL https://api.github.com/repos/rprops/Phenoflow_package/zipball/master
Installing Phenoflow
Installing 1 package: breakaway
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/breakaway_3.0.zip'
Content type 'application/zip' length 72794 bytes (71 KB)
downloaded 71 KB

package ‘breakaway’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: flowClean
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/flowClean_1.12.0.zip'
Content type 'application/zip' length 9758216 bytes (9.3 MB)
downloaded 9.3 MB

package ‘flowClean’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: flowCore
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/flowCore_1.40.6.zip'
Content type 'application/zip' length 18494985 bytes (17.6 MB)
downloaded 17.6 MB

package ‘flowCore’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: flowViz
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/flowViz_1.38.0.zip'
Content type 'application/zip' length 1907890 bytes (1.8 MB)
downloaded 1.8 MB

package ‘flowViz’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: gridExtra
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/gridExtra_2.2.1.zip'
Content type 'application/zip' length 483298 bytes (471 KB)
downloaded 471 KB

package ‘gridExtra’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: mclust
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/mclust_5.2.3.zip'
Content type 'application/zip' length 4149186 bytes (4.0 MB)
downloaded 4.0 MB

package ‘mclust’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: MESS
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/MESS_0.4-15.zip'
Content type 'application/zip' length 3715486 bytes (3.5 MB)
downloaded 3.5 MB

package ‘MESS’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: multcomp
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/multcomp_1.4-6.zip'
Content type 'application/zip' length 631666 bytes (616 KB)
downloaded 616 KB

package ‘multcomp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Installing 1 package: vegan
trying URL 'https://lib.ugent.be/CRAN/bin/windows/contrib/3.3/vegan_2.4-3.zip'
Content type 'application/zip' length 2922042 bytes (2.8 MB)
downloaded 2.8 MB

package ‘vegan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
Downloading GitHub repo lievenclement/flowFDA@master
from URL https://api.github.com/repos/lievenclement/flowFDA/zipball/master
Installing flowFDA
Installing 1 package: flowFP
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/flowFP_1.32.0.zip'
Content type 'application/zip' length 10535362 bytes (10.0 MB)
downloaded 10.0 MB

package ‘flowFP’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\adminmtaghon\AppData\Local\Temp\RtmpmAieiR\downloaded_packages
"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL "C:/Users/adminmtaghon/AppData/Local/Temp/RtmpmAieiR/devtools2cb82ae7c92/lievenclement-flowFDA-03aba88" --library="C:/Program  \
  Files/R/R-3.3.3/library" --install-tests 

* installing *source* package 'flowFDA' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'matrixStats'
Error : package 'flowCore' could not be loaded
ERROR: lazy loading failed for package 'flowFDA'
* removing 'C:/Program Files/R/R-3.3.3/library/flowFDA'
Error: Command failed (1)

The issue appears to still reside in dependencies for flowCore/flowFDA

FMKerckhof commented 7 years ago

Again, after updating R on windows TH.data and sandwichappear to be missing.

setting  value                       
 version  R version 3.4.0 (2017-04-21)
 system   x86_64, mingw32             
 ui       RStudio (1.0.143)           
 language (EN)                        
 collate  Dutch_Belgium.1252          
 tz       Europe/Paris                
 date     2017-05-19                  

Packages --------------------------------------------------------------------------------------------------------------------------------------
 package       * version date       source        
 Biobase         2.36.0  2017-04-25 Bioconductor  
 BiocGenerics    0.22.0  2017-04-25 Bioconductor  
 BiocInstaller   1.26.0  2017-04-25 Bioconductor  
 cluster         2.0.6   2017-03-10 CRAN (R 3.4.0)
 colorspace      1.3-2   2016-12-14 CRAN (R 3.4.0)
 corpcor         1.6.9   2017-04-01 CRAN (R 3.4.0)
 curl            2.6     2017-04-27 CRAN (R 3.4.0)
 DEoptimR        1.0-8   2016-11-19 CRAN (R 3.4.0)
 devtools      * 1.12.0  2016-12-05 CRAN (R 3.4.0)
 digest          0.6.12  2017-01-27 CRAN (R 3.4.0)
 flowCore      * 1.42.0  2017-04-25 Bioconductor  
 flowViz       * 1.40.0  2017-04-25 Bioconductor  
 ggplot2       * 2.2.1   2016-12-30 CRAN (R 3.4.0)
 git2r           0.18.0  2017-01-01 CRAN (R 3.4.0)
 graph           1.54.0  2017-04-25 Bioconductor  
 gtable          0.2.0   2016-02-26 CRAN (R 3.4.0)
 hexbin          1.27.1  2016-12-05 CRAN (R 3.4.0)
 httr            1.2.1   2016-07-03 CRAN (R 3.4.0)
 IDPmisc         1.1.17  2012-11-02 CRAN (R 3.4.0)
 KernSmooth      2.23-15 2015-06-29 CRAN (R 3.4.0)
 lattice       * 0.20-35 2017-03-25 CRAN (R 3.4.0)
 latticeExtra    0.6-28  2016-02-09 CRAN (R 3.4.0)
 lazyeval        0.2.0   2016-06-12 CRAN (R 3.4.0)
 MASS            7.3-47  2017-02-26 CRAN (R 3.4.0)
 matrixStats     0.52.2  2017-04-14 CRAN (R 3.4.0)
 memoise         1.1.0   2017-04-21 CRAN (R 3.4.0)
 munsell         0.4.3   2016-02-13 CRAN (R 3.4.0)
 mvtnorm         1.0-6   2017-03-02 CRAN (R 3.4.0)
 pcaPP           1.9-61  2016-10-11 CRAN (R 3.4.0)
 plyr            1.8.4   2016-06-08 CRAN (R 3.4.0)
 R6              2.2.0   2016-10-05 CRAN (R 3.4.0)
 RColorBrewer    1.1-2   2014-12-07 CRAN (R 3.4.0)
 Rcpp            0.12.10 2017-03-19 CRAN (R 3.4.0)
 robustbase      0.92-7  2016-12-09 CRAN (R 3.4.0)
 rrcov           1.4-3   2016-09-06 CRAN (R 3.4.0)
 scales          0.4.1   2016-11-09 CRAN (R 3.4.0)
 tibble          1.3.0   2017-04-01 CRAN (R 3.4.0)
 withr           1.0.2   2016-06-20 CRAN (R 3.4.0)
rprops commented 7 years ago

Added both packages to imports but this seems to be an issue within another package rather than the core functions of Phenoflow.. Can you try the latest commit?

FMKerckhof commented 7 years ago

Evaluated on a windows7 machine with the following config:

Session info ------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, mingw32             
 ui       RStudio (1.0.153)           
 language (EN)                        
 collate  Dutch_Belgium.1252          
 tz       Europe/Paris                
 date     2017-08-16                  

Packages ----------------------------------------------------------------------------------------------------------------
 package   * version date       source        
 base      * 3.4.1   2017-06-30 local         
 compiler    3.4.1   2017-06-30 local         
 datasets  * 3.4.1   2017-06-30 local         
 devtools  * 1.13.3  2017-08-02 CRAN (R 3.4.1)
 digest      0.6.12  2017-01-27 CRAN (R 3.4.1)
 graphics  * 3.4.1   2017-06-30 local         
 grDevices * 3.4.1   2017-06-30 local         
 memoise     1.1.0   2017-04-21 CRAN (R 3.4.1)
 methods   * 3.4.1   2017-06-30 local         
 stats     * 3.4.1   2017-06-30 local         
 tools       3.4.1   2017-06-30 local         
 utils     * 3.4.1   2017-06-30 local         
 withr       2.0.0   2017-07-28 CRAN (R 3.4.1)

There was no prior Bioconductor installation and installation finished without any errors.