It would be nice to get some support here, and I'll even volunteer to help rectify it if needed.

Error:

cuff<-readCufflinks('diff_out_temp', rebuild = T, gtfFile = 'genes.gtf', genome = 'genome.fa')
Creating database diff_out_temp/cuffData.db
Reading Run Info File diff_out_temp/run.info
Writing runInfo Table
Reading Read Group Info  diff_out_temp/read_groups.info
Writing replicates Table
Reading Var Model Info  diff_out_temp/var_model.info
Writing varModel Table
Reading GTF file
Writing GTF features to 'features' table...
Reading diff_out_temp/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Session info:

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] shinythemes_1.1.1    cummeRbund_2.18.0    Gviz_1.20.0          rtracklayer_1.36.4   GenomicRanges_1.28.4
 [6] GenomeInfoDb_1.12.2  IRanges_2.10.2       S4Vectors_0.14.3     fastcluster_1.1.24   reshape2_1.4.2      
[11] ggplot2_2.2.1        RSQLite_2.0          BiocGenerics_0.22.0  shiny_1.0.5         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12                  Formula_1.2-2                 AnnotationHub_2.8.2          
 [4] knitr_1.17                    XVector_0.16.0                magrittr_1.5                 
 [7] cluster_2.0.6                 GenomicAlignments_1.12.2      splines_3.4.1                
[10] zlibbioc_1.22.0               bit_1.1-12                    BSgenome_1.44.1              
[13] xtable_1.8-2                  colorspace_1.3-2              biovizBase_1.24.0            
[16] lattice_0.20-35               R6_2.2.2                      rlang_0.1.2                  
[19] latticeExtra_0.6-28           ProtGenerics_1.8.0            matrixStats_0.52.2           
[22] htmltools_0.3.6               bit64_0.9-7                   digest_0.6.12                
[25] interactiveDisplayBase_1.14.0 tibble_1.3.4                  Matrix_1.2-10                
[28] acepack_1.4.1                 curl_2.8.1                    RCurl_1.95-4.8               
[31] BiocInstaller_1.26.1          compiler_3.4.1                GenomicFeatures_1.28.4       
[34] scales_0.5.0                  backports_1.1.0               Hmisc_4.0-3                  
[37] Biostrings_2.44.2             Rsamtools_1.28.0              jsonlite_1.5                 
[40] httpuv_1.3.5                  pkgconfig_2.0.1               AnnotationDbi_1.38.2         
[43] munsell_0.4.3                 BiocParallel_1.10.1           httr_1.3.1                   
[46] ensembldb_2.0.4               blob_1.1.0                    plyr_1.8.4                   
[49] stringr_1.2.0                 tools_3.4.1                   dichromat_2.0-0              
[52] nnet_7.3-12                   SummarizedExperiment_1.6.3    data.table_1.10.4            
[55] htmlTable_1.9                 Biobase_2.36.2                gtable_0.2.0                 
[58] checkmate_1.8.3               DBI_0.7                       yaml_2.1.14                  
[61] lazyeval_0.2.0                survival_2.41-3               GenomeInfoDbData_0.99.0      
[64] gridExtra_2.2.1               AnnotationFilter_1.0.0        RColorBrewer_1.1-2           
[67] bitops_1.0-6                  htmlwidgets_0.9               base64enc_0.1-3              
[70] biomaRt_2.32.1                rpart_4.1-11                  mime_0.5                     
[73] memoise_1.1.0                 DelayedArray_0.2.7            stringi_1.1.5                
[76] XML_3.98-1.9                  markdown_0.8                  VariantAnnotation_1.22.3     
[79] foreign_0.8-69