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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

Server side reproducibility of diversity_rf? #37

Closed FMKerckhof closed 5 years ago

FMKerckhof commented 7 years ago

Problem: different plots from div_rf()

FMKerckhof commented 7 years ago

Was ok on linux system with:

Session info -----------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, linux-gnu           
 ui       RStudio (1.0.153)           
 language en_US                       
 collate  en_US.UTF-8                 
 tz       Europe/Brussels             
 date     2017-09-06                  

Packages ---------------------------------------------------------------------------------------------
 package      * version date       source                                   
 base         * 3.4.1   2017-07-08 local                                    
 Biobase        2.36.2  2017-07-27 Bioconductor                             
 BiocGenerics   0.22.0  2017-07-27 Bioconductor                             
 bit            1.1-12  2014-04-09 CRAN (R 3.4.1)                           
 boot           1.3-20  2017-07-30 CRAN (R 3.4.1)                           
 changepoint    2.2.2   2016-10-04 cran (@2.2.2)                            
 cluster        2.0.6   2017-03-16 CRAN (R 3.4.0)                           
 codetools      0.2-15  2016-10-05 CRAN (R 3.3.1)                           
 colorspace     1.3-2   2016-12-14 CRAN (R 3.4.1)                           
 compiler       3.4.1   2017-07-08 local                                    
 corpcor        1.6.9   2017-04-01 cran (@1.6.9)                            
 datasets     * 3.4.1   2017-07-08 local                                    
 DEoptimR       1.0-8   2016-11-19 cran (@1.0-8)                            
 devtools     * 1.13.3  2017-08-02 CRAN (R 3.4.1)                           
 digest         0.6.12  2017-01-27 CRAN (R 3.4.1)                           
 evaluate       0.10.1  2017-06-24 CRAN (R 3.4.1)                           
 flowAI       * 1.4.4   2017-08-16 Bioconductor                             
 flowClean    * 1.14.0  2017-08-10 cran (@1.14.0)                           
 flowCore     * 1.42.2  2017-08-10 cran (@1.42.2)                           
 flowFDA      * 0.99    2017-08-10 Github (lievenclement/flowFDA@03aba88)   
 flowFP       * 1.34.0  2017-08-10 cran (@1.34.0)                           
 flowViz      * 1.40.0  2017-08-10 cran (@1.40.0)                           
 foreach      * 1.4.3   2015-10-13 cran (@1.4.3)                            
 ggplot2      * 2.2.1   2016-12-30 CRAN (R 3.4.1)                           
 graph          1.54.0  2017-08-10 cran (@1.54.0)                           
 graphics     * 3.4.1   2017-07-08 local                                    
 grDevices    * 3.4.1   2017-07-08 local                                    
 grid           3.4.1   2017-07-08 local                                    
 gtable         0.2.0   2016-02-26 CRAN (R 3.4.1)                           
 hexbin         1.27.1  2016-12-05 cran (@1.27.1)                           
 highr          0.6     2016-05-09 CRAN (R 3.4.1)                           
 IDPmisc        1.1.17  2012-11-02 cran (@1.1.17)                           
 iterators      1.0.8   2015-10-13 cran (@1.0.8)                            
 KernSmooth     2.23-15 2015-06-29 CRAN (R 3.4.0)                           
 knitr          1.16    2017-05-18 CRAN (R 3.4.1)                           
 labeling       0.3     2014-08-23 CRAN (R 3.4.1)                           
 lattice      * 0.20-35 2017-03-25 CRAN (R 3.4.0)                           
 latticeExtra   0.6-28  2016-02-09 cran (@0.6-28)                           
 lazyeval       0.2.0   2016-06-12 CRAN (R 3.4.1)                           
 magrittr       1.5     2014-11-22 CRAN (R 3.4.1)                           
 markdown       0.8     2017-04-20 CRAN (R 3.4.1)                           
 MASS         * 7.3-47  2017-04-21 CRAN (R 3.4.0)                           
 Matrix         1.2-11  2017-08-16 CRAN (R 3.4.1)                           
 matrixStats    0.52.2  2017-04-14 cran (@0.52.2)                           
 mclust       * 5.3     2017-05-21 cran (@5.3)                              
 memoise        1.1.0   2017-04-21 CRAN (R 3.4.1)                           
 methods      * 3.4.1   2017-07-08 local                                    
 mime           0.5     2016-07-07 CRAN (R 3.4.1)                           
 multcomp     * 1.4-6   2016-07-14 cran (@1.4-6)                            
 munsell        0.4.3   2016-02-13 CRAN (R 3.4.1)                           
 mvtnorm      * 1.0-6   2017-03-02 cran (@1.0-6)                            
 parallel       3.4.1   2017-07-08 local                                    
 pcaPP          1.9-72  2017-06-27 cran (@1.9-72)                           
 Phenoflow    * 1.1     2017-09-06 Github (rprops/Phenoflow_package@3a60891)
 plyr           1.8.4   2016-06-08 CRAN (R 3.4.1)                           
 RColorBrewer   1.1-2   2014-12-07 CRAN (R 3.4.1)                           
 Rcpp           0.12.12 2017-07-15 CRAN (R 3.4.1)                           
 reshape2       1.4.2   2016-10-22 CRAN (R 3.4.1)                           
 rlang          0.1.2   2017-08-09 CRAN (R 3.4.1)                           
 robustbase     0.92-7  2016-12-09 cran (@0.92-7)                           
 rrcov          1.4-3   2016-09-06 cran (@1.4-3)                            
 sandwich       2.4-0   2017-07-26 cran (@2.4-0)                            
 scales         0.5.0   2017-08-24 cran (@0.5.0)                            
 sfsmisc        1.1-1   2017-06-08 cran (@1.1-1)                            
 splines        3.4.1   2017-07-08 local                                    
 stats        * 3.4.1   2017-07-08 local                                    
 stats4         3.4.1   2017-07-08 local                                    
 stringi        1.1.5   2017-04-07 CRAN (R 3.4.1)                           
 stringr        1.2.0   2017-02-18 CRAN (R 3.4.1)                           
 survival     * 2.41-3  2017-04-04 CRAN (R 3.4.0)                           
 TH.data      * 1.0-8   2017-01-23 cran (@1.0-8)                            
 tibble         1.3.4   2017-08-22 CRAN (R 3.4.1)                           
 tools          3.4.1   2017-07-08 local                                    
 utils        * 3.4.1   2017-07-08 local                                    
 withr          2.0.0   2017-07-28 CRAN (R 3.4.1)                           
 zoo            1.8-0   2017-04-12 cran (@1.8-0)
FMKerckhof commented 7 years ago 
Session info -------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, linux-gnu           
 ui       RStudio (1.0.153)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Europe/Brussels             
 date     2017-09-06                  

Packages -----------------------------------------------------------------------------------------------------------------
 package      * version date       source                                   
 base         * 3.4.1   2017-07-08 local                                    
 Biobase        2.36.2  2017-05-09 Bioconductor                             
 BiocGenerics   0.22.0  2017-05-04 Bioconductor                             
 bit            1.1-12  2014-04-09 CRAN (R 3.4.1)                           
 boot           1.3-20  2017-07-30 CRAN (R 3.4.1)                           
 changepoint    2.2.2   2016-10-04 CRAN (R 3.4.0)                           
 cluster        2.0.6   2017-03-16 CRAN (R 3.4.0)                           
 codetools      0.2-15  2016-10-05 CRAN (R 3.3.1)                           
 colorspace     1.3-2   2016-12-14 CRAN (R 3.4.1)                           
 compiler       3.4.1   2017-07-08 local                                    
 corpcor        1.6.9   2017-04-01 CRAN (R 3.4.1)                           
 datasets     * 3.4.1   2017-07-08 local                                    
 DEoptimR       1.0-8   2016-11-19 CRAN (R 3.4.1)                           
 devtools     * 1.13.3  2017-08-02 CRAN (R 3.4.1)                           
 digest         0.6.12  2017-01-27 CRAN (R 3.4.1)                           
 evaluate       0.10.1  2017-06-24 CRAN (R 3.4.0)                           
 flowAI       * 1.4.4   2017-08-15 Bioconductor                             
 flowClean    * 1.14.0  2017-06-20 cran (@1.14.0)                           
 flowCore     * 1.42.2  2017-07-08 Bioconductor                             
 flowFDA      * 0.99    2016-12-14 Github (lievenclement/flowFDA@03aba88)   
 flowFP       * 1.34.0  2017-05-04 Bioconductor                             
 flowViz      * 1.40.0  2017-05-04 Bioconductor                             
 foreach      * 1.4.3   2015-10-13 CRAN (R 3.4.1)                           
 ggplot2      * 2.2.1   2016-12-30 CRAN (R 3.3.2)                           
 graph          1.54.0  2017-05-04 Bioconductor                             
 graphics     * 3.4.1   2017-07-08 local                                    
 grDevices    * 3.4.1   2017-07-08 local                                    
 grid           3.4.1   2017-07-08 local                                    
 gtable         0.2.0   2016-02-26 CRAN (R 3.4.1)                           
 hexbin         1.27.1  2016-12-05 CRAN (R 3.4.1)                           
 highr          0.6     2016-05-09 CRAN (R 3.4.1)                           
 IDPmisc        1.1.17  2012-11-02 CRAN (R 3.4.1)                           
 iterators      1.0.8   2015-10-13 CRAN (R 3.4.1)                           
 KernSmooth     2.23-15 2015-06-29 CRAN (R 3.4.0)                           
 knitr          1.17    2017-08-10 CRAN (R 3.4.1)                           
 labeling       0.3     2014-08-23 CRAN (R 3.4.1)                           
 lattice      * 0.20-35 2017-03-25 CRAN (R 3.3.3)                           
 latticeExtra   0.6-28  2016-02-09 CRAN (R 3.4.1)                           
 lazyeval       0.2.0   2016-06-12 CRAN (R 3.4.1)                           
 magrittr       1.5     2014-11-22 CRAN (R 3.4.1)                           
 markdown       0.8     2017-04-20 CRAN (R 3.4.0)                           
 MASS         * 7.3-47  2017-04-21 CRAN (R 3.4.0)                           
 Matrix         1.2-11  2017-08-16 CRAN (R 3.4.1)                           
 matrixStats    0.52.2  2017-04-14 CRAN (R 3.4.1)                           
 mclust       * 5.3     2017-05-21 CRAN (R 3.4.0)                           
 memoise        1.1.0   2017-04-21 CRAN (R 3.4.0)                           
 methods      * 3.4.1   2017-07-08 local                                    
 mgcv           1.8-19  2017-08-29 CRAN (R 3.4.1)                           
 mime           0.5     2016-07-07 CRAN (R 3.4.1)                           
 multcomp     * 1.4-6   2016-07-14 CRAN (R 3.3.1)                           
 munsell        0.4.3   2016-02-13 CRAN (R 3.4.1)                           
 mvtnorm      * 1.0-6   2017-03-02 CRAN (R 3.4.1)                           
 nlme           3.1-131 2017-02-06 CRAN (R 3.4.1)                           
 parallel       3.4.1   2017-07-08 local                                    
 pcaPP          1.9-72  2017-06-27 CRAN (R 3.4.0)                           
 permute        0.9-4   2016-09-09 CRAN (R 3.4.1)                           
 Phenoflow    * 1.1     2017-09-06 Github (rprops/Phenoflow_package@33c51fa)
 plyr           1.8.4   2016-06-08 CRAN (R 3.4.1)                           
 RColorBrewer   1.1-2   2014-12-07 CRAN (R 3.4.1)                           
 Rcpp           0.12.12 2017-07-15 CRAN (R 3.4.1)                           
 reshape2       1.4.2   2016-10-22 CRAN (R 3.3.2)                           
 rlang          0.1.2   2017-08-09 CRAN (R 3.4.1)                           
 robustbase     0.92-7  2016-12-09 CRAN (R 3.4.1)                           
 rrcov          1.4-3   2016-09-06 CRAN (R 3.3.1)                           
 sandwich       2.4-0   2017-07-26 CRAN (R 3.4.1)                           
 scales         0.5.0   2017-08-24 CRAN (R 3.4.1)                           
 sfsmisc        1.1-1   2017-06-08 CRAN (R 3.4.0)                           
 splines        3.4.1   2017-07-08 local                                    
 stats        * 3.4.1   2017-07-08 local                                    
 stats4         3.4.1   2017-07-08 local                                    
 stringi        1.1.5   2017-04-07 CRAN (R 3.4.1)                           
 stringr        1.2.0   2017-02-18 CRAN (R 3.4.1)                           
 survival     * 2.41-3  2017-04-04 CRAN (R 3.4.1)                           
 TH.data      * 1.0-8   2017-01-23 CRAN (R 3.4.1)                           
 tibble         1.3.4   2017-08-22 CRAN (R 3.4.1)                           
 tools          3.4.1   2017-07-08 local                                    
 utils        * 3.4.1   2017-07-08 local                                    
 vegan          2.4-4   2017-08-24 CRAN (R 3.4.1)                           
 withr          2.0.0   2017-07-28 CRAN (R 3.4.1)                           
 zoo            1.8-0   2017-04-12 CRAN (R 3.4.1)
FMKerckhof commented 7 years ago

Only difference: liblapack/libblas: Ubuntu where it doesn't work uses openblas

Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so

Where it does work regular blas (unoptimized)

FMKerckhof commented 7 years ago

https://scicomp.stackexchange.com/questions/26137/are-blas-implementations-guaranteed-to-give-the-exact-same-result