diplay error

[SpringBioinformatics]

hi, i have an error when launching this tool and this is the error:

--- Rstudio output : --------------------------------------------------------------------- Passing functions to 'reactive' is deprecated. Please use expressions instead. See ?reactive for more information. Passing functions to 'reactive' is deprecated. Please use expressions instead. See ?reactive for more information. Passing functions to 'reactive' is deprecated. Please use expressions instead. See ?reactive for more information. Passing functions to 'reactive' is deprecated. Please use expressions instead. See ?reactive for more information. Error in lapply(obj, function(val) { : objet 'datasets' introuvable De plus : Message d'avis : In destroyServer(handle) : objet '272451984' introuvable --- Rstudio output end : -----------------------------------------------------------------

And this error maye cause a bad display of the application:

Thank in advance for your help.

[dgrapov]

Can you please show me the sessionInfo()

[SpringBioinformatics]

hi, thank for your response , this this my sessionInfo():

--begin ***

sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages: [1] htmlwidgets_0.5 pheatmap_1.0.7 KEGGREST_1.4.1 pathview_1.4.2 org.Hs.eg.db_2.14.0 KEGGgraph_1.22.1 graph_1.42.0 XML_3.98-1.3
[9] BiocInstaller_1.14.3 hexbin_1.27.1 pcaMethods_1.54.0 Rcpp_0.12.1 qvalue_1.38.0 pls_2.5-0 fdrtool_1.2.15 xts_0.9-7
[17] foreign_0.8-62 Ecdat_0.2-9 Ecfun_0.1-6 AER_1.2-4 sandwich_2.3-3 lmtest_0.9-34 zoo_1.7-12 pwr_1.1-3
[25] RJSONIO_1.3-0 WGCNA_1.47 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2 Biobase_2.24.0 BiocGenerics_0.10.0 RSQLite_1.0.0 DBI_0.3.1
[33] fastcluster_1.1.16 dynamicTreeCut_1.62 impute_1.38.1 wordcloud_2.5 RColorBrewer_1.1-2 pander_0.5.2 lubridate_1.3.3 vegan_2.3-0
[41] permute_0.8-4 reshape2_1.4.1 plyr_1.8.3 rela_4.1 psych_1.5.8 R.utils_2.1.0 R.oo_1.19.0 R.methodsS3_1.7.0
[49] markdown_0.7.7 gridExtra_2.0.0 car_2.0-25 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1 survival_2.37-7 lattice_0.20-29
[57] knitr_1.11 shiny_0.12.2

loaded via a namespace (and not attached): [1] acepack_1.3-3.3 Biostrings_2.32.1 bitops_1.0-6 cluster_2.0.3 codetools_0.2-10 colorspace_1.2-6 curl_0.9.3 digest_0.6.8
[9] doParallel_1.0.8 fda_2.4.4 foreach_1.4.2 GO.db_2.14.0 gtable_0.1.2 htmltools_0.2.6 httpuv_1.3.3 httr_1.0.0
[17] IRanges_1.22.10 iterators_1.0.7 jpeg_0.1-8 jsonlite_0.9.17 latticeExtra_0.6-26 lme4_1.1-9 magrittr_1.5 MASS_7.3-37
[25] Matrix_1.1-5 MatrixModels_0.4-1 matrixStats_0.14.2 memoise_0.2.1 mgcv_1.8-4 mime_0.4 minqa_1.2.4 mnormt_1.5-3
[33] munsell_0.4.2 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-8 pbkrtest_0.4-2 png_0.1-7 preprocessCore_1.26.1 proto_0.3-10
[41] quantreg_5.19 R6_2.1.1 RCurl_1.95-4.7 reshape_0.8.5 Rgraphviz_2.8.1 rpart_4.1-8 rsconnect_0.4.1.4 rstudioapi_0.3.1
[49] scales_0.3.0 slam_0.1-32 SparseM_1.7 stats4_3.1.2 stringi_0.5-5 stringr_1.0.0 tcltk_3.1.2 TeachingDemos_2.9
[57] xtable_1.7-4 XVector_0.4.0 zlibbioc_1.10.0

end *****

[SpringBioinformatics]

This this a good output : ****

sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages: [1] hexbin_1.27.1 pcaMethods_1.54.0 Rcpp_0.12.1 qvalue_1.38.0 pls_2.5-0 fdrtool_1.2.15 xts_0.9-7 foreign_0.8-62
[9] Ecdat_0.2-9 Ecfun_0.1-6 AER_1.2-4 sandwich_2.3-3 lmtest_0.9-34 zoo_1.7-12 pwr_1.1-3 RJSONIO_1.3-0
[17] WGCNA_1.47 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2 Biobase_2.24.0 BiocGenerics_0.10.0 RSQLite_1.0.0 DBI_0.3.1 fastcluster_1.1.16
[25] dynamicTreeCut_1.62 impute_1.38.1 wordcloud_2.5 RColorBrewer_1.1-2 pander_0.5.2 lubridate_1.3.3 vegan_2.3-0 permute_0.8-4
[33] reshape2_1.4.1 plyr_1.8.3 rela_4.1 psych_1.5.8 R.utils_2.1.0 R.oo_1.19.0 R.methodsS3_1.7.0 markdown_0.7.7
[41] gridExtra_2.0.0 car_2.0-25 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1 survival_2.37-7 lattice_0.20-29 knitr_1.11
[49] shiny_0.12.2

loaded via a namespace (and not attached): [1] acepack_1.3-3.3 cluster_2.0.3 codetools_0.2-10 colorspace_1.2-6 digest_0.6.8 doParallel_1.0.8 fda_2.4.4 foreach_1.4.2
[9] GO.db_2.14.0 gtable_0.1.2 htmltools_0.2.6 httpuv_1.3.3 IRanges_1.22.10 iterators_1.0.7 jpeg_0.1-8 jsonlite_0.9.17
[17] latticeExtra_0.6-26 lme4_1.1-9 magrittr_1.5 MASS_7.3-37 Matrix_1.1-5 MatrixModels_0.4-1 matrixStats_0.14.2 memoise_0.2.1
[25] mgcv_1.8-4 mime_0.4 minqa_1.2.4 mnormt_1.5-3 munsell_0.4.2 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-8
[33] pbkrtest_0.4-2 preprocessCore_1.26.1 proto_0.3-10 quantreg_5.19 R6_2.1.1 reshape_0.8.5 rpart_4.1-8 rsconnect_0.4.1.4
[41] rstudioapi_0.3.1 scales_0.3.0 slam_0.1-32 SparseM_1.7 stats4_3.1.2 stringi_0.5-5 stringr_1.0.0 tcltk_3.1.2
[49] TeachingDemos_2.9 xtable_1.7-4

[dgrapov]

What browser are you using?

[dgrapov]

Never mind I see it is the R studio browser. What happens if you select open in browser at the top?

[SpringBioinformatics]

i already used , chromium, opera, firefox ,same error display

[dgrapov]

I'll have to test if is the version of shiny. Can you try version shiny_0.12.1?

[SpringBioinformatics]

same error display with shiny_0.12.1

---

sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages: [1] hexbin_1.27.1 pcaMethods_1.54.0 Rcpp_0.12.1 qvalue_1.38.0 pls_2.5-0 fdrtool_1.2.15 xts_0.9-7 foreign_0.8-62
[9] Ecdat_0.2-9 Ecfun_0.1-6 AER_1.2-4 sandwich_2.3-3 lmtest_0.9-34 zoo_1.7-12 pwr_1.1-3 RJSONIO_1.3-0
[17] WGCNA_1.47 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2 Biobase_2.24.0 BiocGenerics_0.10.0 RSQLite_1.0.0 DBI_0.3.1 fastcluster_1.1.16
[25] dynamicTreeCut_1.62 impute_1.38.1 wordcloud_2.5 RColorBrewer_1.1-2 pander_0.5.2 lubridate_1.3.3 vegan_2.3-0 permute_0.8-4
[33] reshape2_1.4.1 plyr_1.8.3 rela_4.1 psych_1.5.8 R.utils_2.1.0 R.oo_1.19.0 R.methodsS3_1.7.0 markdown_0.7.7
[41] gridExtra_2.0.0 car_2.0-25 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1 survival_2.37-7 lattice_0.20-29 knitr_1.11
[49] shiny_0.12.1

loaded via a namespace (and not attached): [1] acepack_1.3-3.3 cluster_2.0.3 codetools_0.2-10 colorspace_1.2-6 digest_0.6.8 doParallel_1.0.8 fda_2.4.4 foreach_1.4.2
[9] GO.db_2.14.0 gtable_0.1.2 htmltools_0.2.6 httpuv_1.3.3 IRanges_1.22.10 iterators_1.0.7 jpeg_0.1-8 jsonlite_0.9.17
[17] latticeExtra_0.6-26 lme4_1.1-9 magrittr_1.5 MASS_7.3-37 Matrix_1.1-5 MatrixModels_0.4-1 matrixStats_0.14.2 memoise_0.2.1
[25] mgcv_1.8-4 mime_0.4 minqa_1.2.4 mnormt_1.5-3 munsell_0.4.2 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-8
[33] pbkrtest_0.4-2 preprocessCore_1.26.1 proto_0.3-10 quantreg_5.19 R6_2.1.1 reshape_0.8.5 rpart_4.1-8 rsconnect_0.4.1.4
[41] rstudioapi_0.3.1 scales_0.3.0 slam_0.1-32 SparseM_1.7 stats4_3.1.2 stringi_0.5-5 stringr_1.0.0 tcltk_3.1.2
[49] TeachingDemos_2.9 xtable_1.7-4

[SpringBioinformatics]

same error with shiny_0.12.0

---

sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages: [1] hexbin_1.27.1 pcaMethods_1.54.0 Rcpp_0.12.1 qvalue_1.38.0 pls_2.5-0 fdrtool_1.2.15 xts_0.9-7 foreign_0.8-62
[9] Ecdat_0.2-9 Ecfun_0.1-6 AER_1.2-4 sandwich_2.3-3 lmtest_0.9-34 zoo_1.7-12 pwr_1.1-3 RJSONIO_1.3-0
[17] WGCNA_1.47 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2 Biobase_2.24.0 BiocGenerics_0.10.0 RSQLite_1.0.0 DBI_0.3.1 fastcluster_1.1.16
[25] dynamicTreeCut_1.62 impute_1.38.1 wordcloud_2.5 RColorBrewer_1.1-2 pander_0.5.2 lubridate_1.3.3 vegan_2.3-0 permute_0.8-4
[33] reshape2_1.4.1 plyr_1.8.3 rela_4.1 psych_1.5.8 R.utils_2.1.0 R.oo_1.19.0 R.methodsS3_1.7.0 markdown_0.7.7
[41] gridExtra_2.0.0 car_2.0-25 Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1 survival_2.37-7 lattice_0.20-29 knitr_1.11
[49] shiny_0.12.0

loaded via a namespace (and not attached): [1] acepack_1.3-3.3 cluster_2.0.3 codetools_0.2-10 colorspace_1.2-6 digest_0.6.8 doParallel_1.0.8 fda_2.4.4 foreach_1.4.2
[9] GO.db_2.14.0 gtable_0.1.2 htmltools_0.2.6 httpuv_1.3.3 IRanges_1.22.10 iterators_1.0.7 jpeg_0.1-8 jsonlite_0.9.17
[17] latticeExtra_0.6-26 lme4_1.1-9 magrittr_1.5 MASS_7.3-37 Matrix_1.1-5 MatrixModels_0.4-1 matrixStats_0.14.2 memoise_0.2.1
[25] mgcv_1.8-4 mime_0.4 minqa_1.2.4 mnormt_1.5-3 munsell_0.4.2 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-8
[33] pbkrtest_0.4-2 preprocessCore_1.26.1 proto_0.3-10 quantreg_5.19 R6_2.1.1 reshape_0.8.5 rpart_4.1-8 rsconnect_0.4.1.4
[41] rstudioapi_0.3.1 scales_0.3.0 slam_0.1-32 SparseM_1.7 stats4_3.1.2 stringi_0.5-5 stringr_1.0.0 tcltk_3.1.2
[49] TeachingDemos_2.9 xtable_1.7-4

[dgrapov]

Let me run some tests and I'll get back to you.

[SpringBioinformatics]

thank you.

[SpringBioinformatics]

Hi, problem solved by using old version of shiny.

[SpringBioinformatics]

but steel some issues like : (drag-and-drop) options to reorder columns

[dgrapov]

Feel free to make separate issues for any bugs you find :)