I have run DESeq2 successfully on my dataset with several different contrasts; however, when I try to run this one I get the following error:

> dds <- DESeqDataSetFromMatrix(
+     countData = countdata.strict,
+     colData = samples.strict,
+     design = ~ group
+ )
converting counts to integer mode
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 1279 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
> res <- results(dds, contrast = c("group", "HDGSE85", "HDGSE86"))
Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues,  :
  groupHDGSE85 and groupHDGSE86 are expected to be in resultsNames(object)

> resultsNames(dds)
[1] "Intercept"     "groupHDGSE86"  "groupHDGSE87"  "groupHDSGSE85"
> 

"group" in this case indicates sequencing batch. I have run a contrast using "state" already with no problem. Here's what my sample data looks like:

> samples.strict
               group genealine state sex filter.strict filter.relaxed replicate observationid EffectiveAlignmentCount
G002.R1.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         1  G002_CD140_a               151040648
G002.R2.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         2  G002_CD140_b               142144646
G002.R3.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         3  G002_CD140_c               128589118
G002.R4.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         4  G002_CD140_d               152415461
G002.R5.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         5  G002_CD140_e               135059579
G002.R6.CTL HDSGSE85      G002   CTL   M         FALSE          FALSE         6  G002_CD140_f               121105092
G017.R1.HD   HDGSE86      G017    HD   M         FALSE          FALSE         1         SG17a                44082945
G017.R2.HD   HDGSE86      G017    HD   M         FALSE          FALSE         2         SG17b                43321404
G017.R3.HD   HDGSE86      G017    HD   M         FALSE          FALSE         3         SG17c                39897764
G017.R4.HD   HDGSE86      G017    HD   M         FALSE          FALSE         4         SG17e                55759593
G017.R5.HD   HDGSE86      G017    HD   M         FALSE          FALSE         5         SG17f                40662631
G018.R1.HD   HDGSE86      G018    HD   F         FALSE          FALSE         1         SG18a                47275799
G018.R3.HD   HDGSE86      G018    HD   F         FALSE          FALSE         3         SG18c                44562212
G018.R4.HD   HDGSE86      G018    HD   F         FALSE          FALSE         4         SG18d                48443633
G018.R5.HD   HDGSE86      G018    HD   F         FALSE          FALSE         5         SG18f                47221901
G019.R6.CTL  HDGSE87      G019   CTL   F         FALSE          FALSE         6       SG-G19d                23390368
G020.R3.HD   HDGSE87      G020    HD   F         FALSE          FALSE         3       SG-G20a                20107140
>

> sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] calibrate_1.7.2            MASS_7.3-45                genefilter_1.56.0          RColorBrewer_1.1-2       
[5] gplots_3.0.1               DESeq2_1.14.0              SummarizedExperiment_1.4.0 Biobase_2.34.0           
[9] GenomicRanges_1.26.1       GenomeInfoDb_1.10.0        IRanges_2.8.0              S4Vectors_0.12.0         
[13] BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
[1] Rcpp_0.12.7          plyr_1.8.4           XVector_0.14.0       bitops_1.0-6         tools_3.3.1        
[6] zlibbioc_1.20.0      rpart_4.1-10         RSQLite_1.0.0        annotate_1.52.0      gtable_0.2.0       
[11] lattice_0.20-33      Matrix_1.2-6         DBI_0.5-1            gridExtra_2.2.1      cluster_2.0.4      
[16] caTools_1.17.1       gtools_3.5.0         locfit_1.5-9.1       grid_3.3.1           nnet_7.3-12        
[21] data.table_1.9.6     AnnotationDbi_1.36.0 XML_3.98-1.4         survival_2.39-5      BiocParallel_1.8.0 
[26] foreign_0.8-67       gdata_2.17.0         latticeExtra_0.6-28  Formula_1.2-1        geneplotter_1.52.0 
[31] ggplot2_2.1.0        Hmisc_3.17-4         scales_0.4.0         splines_3.3.1        colorspace_1.2-7   
[36] xtable_1.8-2         KernSmooth_2.23-15   acepack_1.4.0        RCurl_1.95-4.8       munsell_0.4.3      
[41] chron_2.3-47

Took me some looking until i saw it:

results(dds, contrast = c("group", "HDGSE85", "HDGSE86"))

But you have labelled one of the groups with an extra 'S': HDSGSE85

This is also why they are in non-alphabetic level order in colData(dds).