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edroaldo / cellrouter

Reconstruction of complex single-cell trajectories using CellRouter
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findpaths function output nearly empty files #1

Open JianmeiZhong opened 6 years ago

JianmeiZhong commented 6 years ago

Hello, I ran findpaths funtion with imputed 10x matrix according to the example with no error before this step.But the 2 generated files in results\paths\SP46.SP* are nearly empty.CellRouter.sh file are complete but executed unsuccessfully with "running command './CellRouter.sh' had status 127" in Rstudio with R 3.4.3 version.Any idea to this issue?

Thanks in advance, Jianmei Zhong

edroaldo commented 6 years ago

Cold you please send me the full error/warning message, your sessionInfo() and also let me know if you have Java installed, and which version?

Thank you so much!

2018-03-19 5:51 GMT-04:00 JianmeiZhong notifications@github.com:

Hello, I ran findpaths funtion with imputed 10x matrix according to the example with no error before this step.But the 2 generated files in results\paths\SP46.SP* are nearly empty.CellRouter.sh file are complete but executed unsuccessfully with "running command './CellRouter.sh' had status 127" in Rstudio with R 3.4.3 version.Any idea to this issue?

Thanks in advance, Jianmei Zhong

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JianmeiZhong commented 6 years ago

okay. Here are several information in Rstudio.

sources [1] "SP_46" getwd() [1] "E:/scRNA-Seq/HP3_outs/scImpute_k4/cellRouter" source('D:/R/R-3.4.3/library/cellrouter-master/CellRouter_Class.R') libdir [1] "D:/R/R-3.4.3/library/cellrouter-master/CellRouter/" cellrouter <- findpaths(cellrouter, libdir, paste(getwd(), 'results/paths', sep='/'), method="graph") --------------------------: SP_46.SP_1 --------------------------: SP_46.SP_2 --------------------------: SP_46.SP_3 --------------------------: SP_46.SP_4 --------------------------: SP_46.SP_5 --------------------------: SP_46.SP_6 --------------------------: SP_46.SP_7 --------------------------: SP_46.SP_8 --------------------------: SP_46.SP_9 --------------------------: SP_46.SP_10 --------------------------: SP_46.SP_11 --------------------------: SP_46.SP_12 --------------------------: SP_46.SP_13 --------------------------: SP_46.SP_14 --------------------------: SP_46.SP_15 --------------------------: SP_46.SP_16 --------------------------: SP_46.SP_17 --------------------------: SP_46.SP_18 --------------------------: SP_46.SP_19 --------------------------: SP_46.SP_20 --------------------------: SP_46.SP_21 --------------------------: SP_46.SP_22 --------------------------: SP_46.SP_23 --------------------------: SP_46.SP_24 --------------------------: SP_46.SP_25 --------------------------: SP_46.SP_26 --------------------------: SP_46.SP_27 --------------------------: SP_46.SP_28 --------------------------: SP_46.SP_29 --------------------------: SP_46.SP_30 --------------------------: SP_46.SP_31 --------------------------: SP_46.SP_32 --------------------------: SP_46.SP_33 --------------------------: SP_46.SP_34 --------------------------: SP_46.SP_35 --------------------------: SP_46.SP_36 --------------------------: SP_46.SP_37 --------------------------: SP_46.SP_38 --------------------------: SP_46.SP_39 --------------------------: SP_46.SP_40 --------------------------: SP_46.SP_41 --------------------------: SP_46.SP_42 --------------------------: SP_46.SP_43 --------------------------: SP_46.SP_44 --------------------------: SP_46.SP_45 --------------------------: SP_46.SP_47 --------------------------: SP_46.SP_48 --------------------------: SP_46.SP_49 --------------------------: SP_46.SP_50 --------------------------: SP_46.SP_51 --------------------------: SP_46.SP_52 --------------------------: SP_46.SP_53 --------------------------: SP_46.SP_54 --------------------------: SP_46.SP_55 --------------------------: SP_46.SP_56 --------------------------: SP_46.SP_57 --------------------------: SP_46.SP_58 --------------------------: SP_46.SP_59 --------------------------: SP_46.SP_60 --------------------------: SP_46.SP_61 --------------------------: SP_46.SP_62 --------------------------: SP_46.SP_63 --------------------------: SP_46.SP_64 --------------------------: SP_46.SP_65 There were 50 or more warnings (use warnings() to see the first 50) warnings() warnings： 1: running command './CellRouter.sh' had status 127 2: running command './CellRouter.sh' had status 127 3: running command './CellRouter.sh' had status 127 4: running command './CellRouter.sh' had status 127 5: running command './CellRouter.sh' had status 127 6: running command './CellRouter.sh' had status 127 7: running command './CellRouter.sh' had status 127 8: running command './CellRouter.sh' had status 127 9: running command './CellRouter.sh' had status 127 10: running command './CellRouter.sh' had status 127 11: running command './CellRouter.sh' had status 127 12: running command './CellRouter.sh' had status 127 13: running command './CellRouter.sh' had status 127 14: running command './CellRouter.sh' had status 127 15: running command './CellRouter.sh' had status 127 16: running command './CellRouter.sh' had status 127 17: running command './CellRouter.sh' had status 127 18: running command './CellRouter.sh' had status 127 19: running command './CellRouter.sh' had status 127 20: running command './CellRouter.sh' had status 127 21: running command './CellRouter.sh' had status 127 22: running command './CellRouter.sh' had status 127 23: running command './CellRouter.sh' had status 127 24: running command './CellRouter.sh' had status 127 25: running command './CellRouter.sh' had status 127 26: running command './CellRouter.sh' had status 127 27: running command './CellRouter.sh' had status 127 28: running command './CellRouter.sh' had status 127 29: running command './CellRouter.sh' had status 127 30: running command './CellRouter.sh' had status 127 31: running command './CellRouter.sh' had status 127 32: running command './CellRouter.sh' had status 127 33: running command './CellRouter.sh' had status 127 34: running command './CellRouter.sh' had status 127 35: running command './CellRouter.sh' had status 127 36: running command './CellRouter.sh' had status 127 37: running command './CellRouter.sh' had status 127 38: running command './CellRouter.sh' had status 127 39: running command './CellRouter.sh' had status 127 40: running command './CellRouter.sh' had status 127 41: running command './CellRouter.sh' had status 127 42: running command './CellRouter.sh' had status 127 43: running command './CellRouter.sh' had status 127 44: running command './CellRouter.sh' had status 127 45: running command './CellRouter.sh' had status 127 46: running command './CellRouter.sh' had status 127 47: running command './CellRouter.sh' had status 127 48: running command './CellRouter.sh' had status 127 49: running command './CellRouter.sh' had status 127 50: running command './CellRouter.sh' had status 127 system("results/paths/SP_46.SP_1/CellRouter.sh") Warning message: running command 'results/paths/SP_46.SP_1/CellRouter.sh' had status 127 system("sh results/paths/SP_46.SP_1/CellRouter.sh") results/paths/SP_46.SP_1/CellRouter.sh: line 3: $'\r': command not found results/paths/SP_46.SP_1/CellRouter.sh: line 5: $'\r': command not found results/paths/SP_46.SP_1/CellRouter.sh: line 6: $'\r': command not found 1) Computing flow network error: cannot find or load the main class cellrouter.CellRouter. dir("results/paths/SP_46.SP_1/") [1] "cell_sinks.txt" "cell_sources.txt" "CellRouter.sh"
the *.txt file are size of 1kb containing one cell barcode seemingly and the sessionInfo(): sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] RColorBrewer_1.1-2 proxy_0.4-21 cccd_1.5 org.Hs.eg.db_3.5.0
[5] GO.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0
[9] Biobase_2.38.0 BiocGenerics_0.24.0 gplots_3.0.1 mclust_5.4
[13] ggplot2_2.2.1 plyr_1.8.4 igraph_1.1.2 tsne_0.1-3
[17] plotrix_3.7 DOSE_3.5.1 pheatmap_1.0.8 reshape2_1.4.3
[21] reshape_0.8.7

loaded via a namespace (and not attached): [1] Rcpp_0.12.15 FNN_1.1 deldir_0.1-14 gtools_3.5.0 digest_0.6.14
[6] RSQLite_2.0 pillar_1.1.0 rlang_0.1.6 lazyeval_0.2.1 data.table_1.10.4-3 [11] gdata_2.18.0 blob_1.1.0 qvalue_2.10.0 labeling_0.3 splines_3.4.3
[16] BiocParallel_1.12.0 stringr_1.2.0 bit_1.1-12 munsell_0.4.3 fgsea_1.4.1
[21] compiler_3.4.3 pkgconfig_2.0.1 tibble_1.4.2 gridExtra_2.3 bitops_1.0-6
[26] gtable_0.2.0 DBI_0.7 magrittr_1.5 scales_0.5.0 KernSmooth_2.23-15 [31] stringi_1.1.6 GOSemSim_2.4.1 DO.db_2.9 fastmatch_1.1-0 tools_3.4.3
[36] bit64_0.9-7 colorspace_1.3-2 caTools_1.17.1 memoise_1.1.0

Following are version of java and it's installed and configured successfully: $ java -version java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

Thanks a lot!

edroaldo commented 6 years ago

I see... thank you your answer. It is not possible to run .sh scripts in Windows. The script has to be converted in a BATCH script that Windows can understand and then run. I am sorry, I am not a Windows user. Give me a few days to figure out an strategy to overcome this limitation.

Thanks for your patience!

2018-03-19 9:38 GMT-04:00 JianmeiZhong notifications@github.com:

okay. Here are several information in Rstudio.

sources [1] "SP_46" getwd() [1] "E:/scRNA-Seq/HP3_outs/scImpute_k4/cellRouter" source('D:/R/R-3.4.3/library/cellrouter-master/CellRouter_Class.R') libdir [1] "D:/R/R-3.4.3/library/cellrouter-master/CellRouter/" cellrouter <- findpaths(cellrouter, libdir, paste(getwd(), 'results/paths', sep='/'), method="graph") --------------------------: SP_46.SP_1 --------------------------: SP_46.SP_2 --------------------------: SP_46.SP_3 --------------------------: SP_46.SP_4 --------------------------: SP_46.SP_5 --------------------------: SP_46.SP_6 --------------------------: SP_46.SP_7 --------------------------: SP_46.SP_8 https://maps.google.com/?q=46.SP_8&entry=gmail&source=g --------------------------: SP_46.SP_9 --------------------------: SP_46.SP_10 --------------------------: SP_46.SP_11 --------------------------: SP_46.SP_12 --------------------------: SP_46.SP_13 --------------------------: SP_46.SP_14 --------------------------: SP_46.SP_15 https://maps.google.com/?q=46.SP_15&entry=gmail&source=g --------------------------: SP_46.SP_16 --------------------------: SP_46.SP_17 https://maps.google.com/?q=46.SP_17&entry=gmail&source=g --------------------------: SP_46.SP_18 --------------------------: SP_46.SP_19 --------------------------: SP_46.SP_20 --------------------------: SP_46.SP_21 --------------------------: SP_46.SP_22 --------------------------: SP_46.SP_23 --------------------------: SP_46.SP_24 --------------------------: SP_46.SP_25 --------------------------: SP_46.SP_26 --------------------------: SP_46.SP_27 --------------------------: SP_46.SP_28 --------------------------: SP_46.SP_29 --------------------------: SP_46.SP_30 --------------------------: SP_46.SP_31 https://maps.google.com/?q=46.SP_31&entry=gmail&source=g --------------------------: SP_46.SP_32 --------------------------: SP_46.SP_33 --------------------------: SP_46.SP_34 --------------------------: SP_46.SP_35 --------------------------: SP_46.SP_36 https://maps.google.com/?q=46.SP_36&entry=gmail&source=g --------------------------: SP_46.SP_37 --------------------------: SP_46.SP_38 --------------------------: SP_46.SP_39 https://maps.google.com/?q=46.SP_39+%0D%0A--------------------------:+SP&entry=gmail&source=g --------------------------: SP_46.SP_40 --------------------------: SP_46.SP_41 --------------------------: SP_46.SP_42 --------------------------: SP_46.SP_43 https://maps.google.com/?q=46.SP_43&entry=gmail&source=g --------------------------: SP_46.SP_44 --------------------------: SP_46.SP_45 --------------------------: SP_46.SP_47 --------------------------: SP_46.SP_48 --------------------------: SP_46.SP_49 --------------------------: SP_46.SP_50 https://maps.google.com/?q=46.SP_50+%0D%0A--------------------------:+SP&entry=gmail&source=g --------------------------: SP_46.SP_51 --------------------------: SP_46.SP_52 --------------------------: SP_46.SP_53 --------------------------: SP_46.SP_54 --------------------------: SP_46.SP_55 https://maps.google.com/?q=46.SP_55&entry=gmail&source=g --------------------------: SP_46.SP_56 https://maps.google.com/?q=SP_56+%0D%0A--------------------------:+SP_46.SP&entry=gmail&source=g --------------------------: SP_46.SP_57 --------------------------: SP_46.SP_58 https://maps.google.com/?q=46.SP_58+%0D%0A--------------------------:+SP&entry=gmail&source=g --------------------------: SP_46.SP_59 --------------------------: SP_46.SP_60 https://maps.google.com/?q=46.SP_60+%0D%0A--------------------------:+SP&entry=gmail&source=g --------------------------: SP_46.SP_61 --------------------------: SP_46.SP_62 https://maps.google.com/?q=46.SP_62+%0D%0A--------------------------:+SP&entry=gmail&source=g --------------------------: SP_46.SP_63 https://maps.google.com/?q=SP_63+%0D%0A--------------------------:+SP_46&entry=gmail&source=g --------------------------: SP_46.SP_64 --------------------------: SP_46.SP_65 https://maps.google.com/?q=46.SP_65&entry=gmail&source=g There were 50 or more warnings (use warnings() to see the first 50) warnings() warnings： 1: running command './CellRouter.sh' had status 127 2: running command './CellRouter.sh' had status 127 3: running command './CellRouter.sh' had status 127 4: running command './CellRouter.sh' had status 127 5: running command './CellRouter.sh' had status 127 6: running command './CellRouter.sh' had status 127 7: running command './CellRouter.sh' had status 127 8: running command './CellRouter.sh' had status 127 9: running command './CellRouter.sh' had status 127 10: running command './CellRouter.sh' had status 127 11: running command './CellRouter.sh' had status 127 12: running command './CellRouter.sh' had status 127 13: running command './CellRouter.sh' had status 127 14: running command './CellRouter.sh' had status 127 15: running command './CellRouter.sh' had status 127 16: running command './CellRouter.sh' had status 127 17: running command './CellRouter.sh' had status 127 18: running command './CellRouter.sh' had status 127 19: running command './CellRouter.sh' had status 127 20: running command './CellRouter.sh' had status 127 21: running command './CellRouter.sh' had status 127 22: running command './CellRouter.sh' had status 127 23: running command './CellRouter.sh' had status 127 24: running command './CellRouter.sh' had status 127 25: running command './CellRouter.sh' had status 127 26: running command './CellRouter.sh' had status 127 27: running command './CellRouter.sh' had status 127 28: running command './CellRouter.sh' had status 127 29: running command './CellRouter.sh' had status 127 30: running command './CellRouter.sh' had status 127 31: running command './CellRouter.sh' had status 127 32: running command './CellRouter.sh' had status 127 33: running command './CellRouter.sh' had status 127 34: running command './CellRouter.sh' had status 127 35: running command './CellRouter.sh' had status 127 36: running command './CellRouter.sh' had status 127 37: running command './CellRouter.sh' had status 127 38: running command './CellRouter.sh' had status 127 39: running command './CellRouter.sh' had status 127 40: running command './CellRouter.sh' had status 127 41: running command './CellRouter.sh' had status 127 42: running command './CellRouter.sh' had status 127 43: running command './CellRouter.sh' had status 127 44: running command './CellRouter.sh' had status 127 45: running command './CellRouter.sh' had status 127 46: running command './CellRouter.sh' had status 127 47: running command './CellRouter.sh' had status 127 48: running command './CellRouter.sh' had status 127 49: running command './CellRouter.sh' had status 127 50: running command './CellRouter.sh' had status 127 system("results/paths/SP_46.SP_1/CellRouter.sh") Warning message: running command 'results/paths/SP_46.SP_1/CellRouter.sh' had status 127 system("sh results/paths/SP_46.SP_1/CellRouter.sh") results/paths/SP_46.SP_1/CellRouter.sh: line 3: $'\r': command not found results/paths/SP_46.SP_1/CellRouter.sh: line 5: $'\r': command not found results/paths/SP_46.SP_1/CellRouter.sh: line 6: $'\r': command not found

  1. Computing flow network error: cannot find or load the main class cellrouter.CellRouter.

dir("results/paths/SP_46.SP_1/") [1] "cell_sinks.txt" "cell_sources.txt" "CellRouter.sh" the *.txt file are size of 1kb containing one cell barcode seemingly and the sessionInfo(): sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] RColorBrewer_1.1-2 proxy_0.4-21 cccd_1.5 org.Hs.eg.db_3.5.0 [5] GO.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [9] Biobase_2.38.0 BiocGenerics_0.24.0 gplots_3.0.1 mclust_5.4 [13] ggplot2_2.2.1 plyr_1.8.4 igraph_1.1.2 tsne_0.1-3 [17] plotrix_3.7 DOSE_3.5.1 pheatmap_1.0.8 reshape2_1.4.3 [21] reshape_0.8.7

loaded via a namespace (and not attached): [1] Rcpp_0.12.15 FNN_1.1 deldir_0.1-14 gtools_3.5.0 digest_0.6.14 [6] RSQLite_2.0 pillar_1.1.0 rlang_0.1.6 lazyeval_0.2.1 data.table_1.10.4-3 [11] gdata_2.18.0 blob_1.1.0 qvalue_2.10.0 labeling_0.3 splines_3.4.3 [16] BiocParallel_1.12.0 stringr_1.2.0 bit_1.1-12 munsell_0.4.3 fgsea_1.4.1 [21] compiler_3.4.3 pkgconfig_2.0.1 tibble_1.4.2 gridExtra_2.3 bitops_1.0-6 [26] gtable_0.2.0 DBI_0.7 magrittr_1.5 scales_0.5.0 KernSmooth_2.23-15 [31] stringi_1.1.6 GOSemSim_2.4.1 DO.db_2.9 fastmatch_1.1-0 tools_3.4.3 [36] bit64_0.9-7 colorspace_1.3-2 caTools_1.17.1 memoise_1.1.0

Following are version of java and it's installed and configured successfully: $ java -version java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

Thanks a lot!

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JianmeiZhong commented 6 years ago

Oh,Maybe i should try to run this script in linux system.I didn't notice the demand for running system.thanks for your reply. Hope for your update.

edroaldo commented 6 years ago

If you can run this in Linux is better. Please, try to do so. I will update the github webpage to contain more information about systems requirements.

Thanks a lot!

On Mon, Mar 19, 2018, 9:35 PM JianmeiZhong notifications@github.com wrote:

Oh,Maybe i should try to run this script in linux system.I didn't notice the demand for running system.thanks for your reply. Hope for your update.

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JianmeiZhong commented 6 years ago

Hi, Sorry to bother you again.I was thrown same errors when ran script on linux (Linux version 2.6.32-358.el6.x86_64 (mockbuild@x86-022.build.eng.bos.redhat.com) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC) ) as the previous time .I installed successfully almost every package you mentioned but "scde" since the depended "Cairo" package are a little hard to install(I'll complete installing it later or when the command complain of lacking it ).I didn't figure out how to fix below information.is Java installed improperly?Would you guide me some helpful resolutions?Thanks in advance.

cellrouter <- findpaths(cellrouter, libdir, paste(getwd(), 'results/paths', sep='/'), method="graph") --------------------------: SP_46.SP_1 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_2 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_3 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_4 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_5 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_6 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_7 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_8 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_9 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_10 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_11 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_12 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_13 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_14 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_15 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_16 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_17 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_18 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_19 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_20 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_21 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_22 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_23 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_24 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_25 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_26 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_27 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_28 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_29 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_30 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_31 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_32 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_33 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_34 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_35 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_36 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_37 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_38 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_39 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_40 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_41 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_42 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_43 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_44 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_45 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_47 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_48 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_49 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_50 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_51 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_52 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_53 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_54 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_55 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_56 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_57 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_58 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_59 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_60 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_61 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_62 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_63 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_64 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_65 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter system('./results/paths/SP_46.SP_1/CellRouter.sh') 1) Computing flow network Creating flow network... Uncaught exception - null java.lang.NullPointerException at cellrouter.CellRouterUtils.getSourcesSinks(CellRouterUtils.java:48) at cellrouter.CellRouter.createFlowNetwork(CellRouter.java:76) at cellrouter.CellRouter.runAnalysis(CellRouter.java:63) at cellrouter.CellRouter.main(CellRouter.java:244) sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

Matrix products: default BLAS/LAPACK: /home/zjm/miniconda3/lib/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] RColorBrewer_1.1-2 org.Hs.eg.db_3.5.0 BiocInstaller_1.28.0 [4] proxy_0.4-21 cccd_1.5 GO.db_3.5.0 [7] AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [10] Biobase_2.38.0 BiocGenerics_0.24.0 gplots_3.0.1 [13] mclust_5.4 ggplot2_2.2.1 plyr_1.8.4 [16] igraph_1.2.1 tsne_0.1-3 plotrix_3.7 [19] ReactomePA_1.22.0 clusterProfiler_3.6.0 DOSE_3.4.0 [22] pheatmap_1.0.8 reshape2_1.4.3 reshape_0.8.7

loaded via a namespace (and not attached): [1] httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [4] splines_3.4.3 gtools_3.5.0 DO.db_2.9 [7] rvcheck_0.0.9 blob_1.1.0 pillar_1.2.1 [10] RSQLite_2.0 backports_1.1.2 glue_1.2.0 [13] digest_0.6.15 checkmate_1.8.5 qvalue_2.10.0 [16] colorspace_1.3-2 pkgconfig_2.0.1 reactome.db_1.62.0 [19] purrr_0.2.4 scales_0.5.0 gdata_2.18.0 [22] BiocParallel_1.12.0 tibble_1.4.2 lazyeval_0.2.1 [25] magrittr_1.5 deldir_0.1-14 memoise_1.1.0 [28] FNN_1.1 graph_1.56.0 tools_3.4.3 [31] data.table_1.10.4-3 stringr_1.3.0 munsell_0.4.3 [34] compiler_3.4.3 caTools_1.17.1 rlang_0.2.0 [37] rappdirs_0.3.1 bitops_1.0-6 labeling_0.3 [40] gtable_0.2.0 DBI_0.8 R6_2.2.2 [43] gridExtra_2.3 graphite_1.24.1 bit_1.1-12 [46] fastmatch_1.1-0 fgsea_1.4.1 KernSmooth_2.23-15 [49] GOSemSim_2.4.1 stringi_1.1.7 Rcpp_0.12.16

edroaldo commented 6 years ago

Hi Jianmei,

No worries! You do not bother me! I am sorry you are running into issues. I have actually updated the github webpage to be more explicit about systems requirements. scde is actually not required. I need to remove from the CellRouter code and push this change to github.

Could you please send me your Java version?

You have the Oracle Java not the OpenJDK. For some reason, the Java code only works on the Oracle JDK. This link contains instructions to install the Oracle JDK:

https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-get-on-ubuntu-16-04

Also, please install the following:

install.packages("Vennerable", repos="http://R-Forge.R-project.org")

Please, let me know if that solve your problem. Thanks for your patience while trying CellRouter.

Thanks!

2018-03-23 14:13 GMT-04:00 JianmeiZhong notifications@github.com:

Hi, Sorry to bother you again.I was thrown same errors when ran script on linux (Linux version 2.6.32-358.el6.x86_64 (mockbuild@x86-022.build.eng. bos.redhat.com) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC) ) as the previous time .I installed successfully almost every package you mentioned but "scde" since the depended "Cairo" package are a little hard to install(I'll complete installing it later or when the command complain of lacking it ).I didn't figure out how to fix below information.is Java installed improperly?Would you guide me some helpful resolutions?Thanks in advance.

cellrouter <- findpaths(cellrouter, libdir, paste(getwd(), 'results/paths', sep='/'), method="graph") --------------------------: SP_46.SP_1

  1. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_2
  2. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_3
  3. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_4
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  5. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_6
  6. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_7
  7. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_8
  8. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_9
  9. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_10
  10. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_11
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  34. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_35
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  40. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_41
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  45. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_47
  46. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_48
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  53. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_55
  54. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_56 https://maps.google.com/?q=46.SP_56&entry=gmail&source=g
  55. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_57
  56. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_58
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  63. Computing flow network Error: Could not find or load main class cellrouter.CellRouter --------------------------: SP_46.SP_65
  64. Computing flow network Error: Could not find or load main class cellrouter.CellRouter

system('./results/paths/SP_46.SP_1/CellRouter.sh')

  1. Computing flow network Creating flow network... Uncaught exception - null java.lang.NullPointerException at cellrouter.CellRouterUtils.getSourcesSinks(CellRouterUtils.java:48) at cellrouter.CellRouter.createFlowNetwork(CellRouter.java:76) at cellrouter.CellRouter.runAnalysis(CellRouter.java:63) at cellrouter.CellRouter.main(CellRouter.java:244)

sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

Matrix products: default BLAS/LAPACK: /home/zjm/miniconda3/lib/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] RColorBrewer_1.1-2 org.Hs.eg.db_3.5.0 BiocInstaller_1.28.0 [4] proxy_0.4-21 cccd_1.5 GO.db_3.5.0 [7] AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [10] Biobase_2.38.0 BiocGenerics_0.24.0 gplots_3.0.1 [13] mclust_5.4 ggplot2_2.2.1 plyr_1.8.4 [16] igraph_1.2.1 tsne_0.1-3 plotrix_3.7 [19] ReactomePA_1.22.0 clusterProfiler_3.6.0 DOSE_3.4.0 [22] pheatmap_1.0.8 reshape2_1.4.3 reshape_0.8.7

loaded via a namespace (and not attached): [1] httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [4] splines_3.4.3 gtools_3.5.0 DO.db_2.9 [7] rvcheck_0.0.9 blob_1.1.0 pillar_1.2.1 [10] RSQLite_2.0 backports_1.1.2 glue_1.2.0 [13] digest_0.6.15 checkmate_1.8.5 qvalue_2.10.0 [16] colorspace_1.3-2 pkgconfig_2.0.1 reactome.db_1.62.0 [19] purrr_0.2.4 scales_0.5.0 gdata_2.18.0 [22] BiocParallel_1.12.0 tibble_1.4.2 lazyeval_0.2.1 [25] magrittr_1.5 deldir_0.1-14 memoise_1.1.0 [28] FNN_1.1 graph_1.56.0 tools_3.4.3 [31] data.table_1.10.4-3 stringr_1.3.0 munsell_0.4.3 [34] compiler_3.4.3 caTools_1.17.1 rlang_0.2.0 [37] rappdirs_0.3.1 bitops_1.0-6 labeling_0.3 [40] gtable_0.2.0 DBI_0.8 R6_2.2.2 [43] gridExtra_2.3 graphite_1.24.1 bit_1.1-12 [46] fastmatch_1.1-0 fgsea_1.4.1 KernSmooth_2.23-15 [49] GOSemSim_2.4.1 stringi_1.1.7 Rcpp_0.12.16

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JianmeiZhong commented 6 years ago

Okay.Thanks your patience too :) Same error occurred even after installing/updating Java.previous version of Java didn't been recorded but present Java are: [zjm@ data]$ java -version java version "1.8.0_172-ea" Java(TM) SE Runtime Environment (build 1.8.0_172-ea-b03) Java HotSpot(TM) Server VM (build 25.172-b03, mixed mode) [zjm@ data]$ javac -version javac 1.8.0_172-ea [root@ jdk1.8.0_172]$ yum list installed |grep java ant-javamail.x86_64 1.7.1-13.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 eclipse-mylyn-java.x86_64 3.4.2-9.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 gcc-java.x86_64 4.4.7-18.el6 @base java-1.8.0-openjdk.x86_64 1:1.8.0.161-3.b14.el6_9 @updates java-1.8.0-openjdk-headless.x86_64 1:1.8.0.161-3.b14.el6_9 @updates java_cup.x86_64 1:0.10k-5.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 libvirt-java.noarch 0.4.9-1.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 libvirt-java-devel.noarch 0.4.9-1.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 lpg-java-compat.noarch 1.1.0-4.1.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 mysql-connector-java.noarch 1:5.1.17-6.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 pki-java-tools.noarch 9.0.3-30.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 subversion-javahl.x86_64 1.6.11-7.el6 @anaconda-RedHatEnterpriseLinux-201301301459.x86_64/6.4 tzdata-java.noarch 2018c-1.el6 @updates

I followed http://openjdk.java.net/install/ and set the JAVA_HOME after installation because my system don't have apt-get but yum.

edroaldo commented 6 years ago

It seems that you have installed openJDK and not the Oracle JDK. As I mentioned before, It will only work with the Oracle JDK. Please, try to follow the instructions in the section Install Oracle Java 8 JRE of this webpage: https://www.digitalocean.com/community/tutorials/how-to-install-java-on-centos-and-fedora

Then, you need to unsure that your system is using the Oracle Java not the openJDK one. You can follow instruction in the following link to set which Java your computer is using: https://askubuntu.com/questions/315646/update-java-alternatives-vs-update-alternatives-config-java

Please, let me know if that works.

Thanks!

2018-03-24 5:33 GMT-04:00 JianmeiZhong notifications@github.com:

Okay.Thanks your patience too :) Same error occurred even after installing/updating Java.previous version of Java didn't been recorded but present Java are: [zjm@ data]$ java -version java version "1.8.0_172-ea" Java(TM) SE Runtime Environment (build 1.8.0_172-ea-b03) Java HotSpot(TM) Server VM (build 25.172-b03, mixed mode) [zjm@ data]$ javac -version javac 1.8.0_172-ea [root@ jdk1.8.0_172]$ yum list installed |grep java ant-javamail.x86_64 1.7.1-13.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 eclipse-mylyn-java.x86_64 3.4.2-9.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 gcc-java.x86_64 4.4.7-18.el6 @base https://github.com/base java-1.8.0-openjdk.x86_64 1:1.8.0.161-3.b14.el6_9 @updates https://github.com/updates java-1.8.0-openjdk-headless.x86_64 1:1.8.0.161-3.b14.el6_9 @updates https://github.com/updates java_cup.x86_64 1:0.10k-5.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 libvirt-java.noarch 0.4.9-1.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 libvirt-java-devel.noarch 0.4.9-1.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 lpg-java-compat.noarch 1.1.0-4.1.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 mysql-connector-java.noarch 1:5.1.17-6.el6 @anaconda- RedHatEnterpriseLinux-201301301459.x86_64/6.4 pki-java-tools.noarch 9.0.3-30.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 subversion-javahl.x86_64 1.6.11-7.el6 @anaconda-RedHatEnterpriseLinux- 201301301459.x86_64/6.4 tzdata-java.noarch 2018c-1.el6 @updates https://github.com/updates

I followed http://openjdk.java.net/install/ and set the JAVA_HOME after installation because my system don't have apt-get but yum.

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JianmeiZhong commented 6 years ago

Hi, After openJDK replaced by oracle JDK 9,the findpaths function works now!!! :) Thanks for your guidance sincerely. :)

best, Jianmei Zhong

edroaldo commented 6 years ago

Fantastic! Thanks for your interest in our work! Let me know if can be of further help.

Thanks!

2018-03-29 2:50 GMT-04:00 JianmeiZhong notifications@github.com:

Hi, After openJDK replaced by oracle JDK 9,the findpaths function works now!!! :) Thanks for your guidance sincerely. :)

best, Jianmei Zhong

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