I want to add the annotation row labelling to a pheatmap.

It appears from the tutorial here: https://towardsdatascience.com/pheatmap-draws-pretty-heatmaps-483dab9a3cc

That I can call a data frame in order to do this.

Here is my data frame:

               Sample Condition
1    Sample_Run1HR62_S1_Run1    groupa
2    Sample_Run2HR62_S1_Run2    groupa
3    Sample_Run1HR70_S2_Run1    groupa
4    Sample_Run2HR70_S2_Run2    groupa
5    Sample_Run1HR78_S3_Run1    groupa
6    Sample_Run2HR78_S3_Run2    groupa
7    Sample_Run1HR81_S4_Run1    groupa
8    Sample_Run2HR81_S4_Run2    groupa
9    Sample_Run1HR87_S5_Run1    groupa
10   Sample_Run2HR87_S5_Run2    groupa
11   Sample_Run1HR99_S6_Run1    groupa
12   Sample_Run2HR99_S6_Run2    groupa
13  Sample_Run1HR107_S7_Run1    groupa
14  Sample_Run2HR107_S7_Run2    groupa
15  Sample_Run1HR114_S8_Run1    groupa
16  Sample_Run2HR114_S8_Run2    groupa
17 Sample_Run1HR142_S17_Run1    groupa
18 Sample_Run2HR142_S17_Run2    groupa
19 Sample_Run1HR146_S18_Run1    groupa
20 Sample_Run2HR146_S18_Run2    groupa
21   Sample_Run1HR61_S9_Run1    groupb
22   Sample_Run2HR61_S9_Run2    groupb
23  Sample_Run1HR71_S11_Run1    groupb
24  Sample_Run2HR71_S11_Run2    groupb
25  Sample_Run1HR74_S41_Run1    groupb
26  Sample_Run2HR74_S41_Run2    groupb
27  Sample_Run1HR80_S12_Run1    groupb
28  Sample_Run2HR80_S12_Run2    groupb
29  Sample_Run1HR86_S13_Run1    groupb
30  Sample_Run2HR86_S13_Run2    groupb
31 Sample_Run1HR115_S14_Run1    groupb
32 Sample_Run2HR115_S14_Run2    groupb
33 Sample_Run1HR121_S15_Run1    groupb
34 Sample_Run2HR121_S15_Run2    groupb
35 Sample_Run1HR127_S16_Run1    groupb
36 Sample_Run2HR127_S16_Run2    groupb
37  Sample_Run2HR66_S10_Run2    groupb
38  Sample_Run1HR66_S10_Run1    groupb

Here is the r script I am using to generate the Pheatmap:

# Create sample-sample heatmap
sampleDists <- dist(t(assay(rld))) #calculates Euclidean distance. Rld to ensure we have a roughly equal contribution from all genes
sampleDistMatrix <- as.matrix( sampleDists )
rownames(sampleDistMatrix) <- paste( targets$Sample, sep = " - " )
colnames(sampleDistMatrix) <- NULL
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
pheatmap(sampleDistMatrix, clustering_distance_rows = sampleDists, clustering_distance_cols = sampleDists,col = colors, main = "Heatmap of Sample to Sample Distances in Pig Samples" )

Here is the same code when I add the 'annotation_row' command:

# Create sample-sample heatmap
sampleDists <- dist(t(assay(rld))) #calculates Euclidean distance. Rld to ensure we have a roughly equal contribution from all genes
sampleDistMatrix <- as.matrix( sampleDists )
rownames(sampleDistMatrix) <- paste( targets$Sample, sep = " - " )
colnames(sampleDistMatrix) <- NULL
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
pheatmap(sampleDistMatrix, clustering_distance_rows = sampleDists, clustering_distance_cols = sampleDists,col = colors,annotation_row = targets, main = "Heatmap of Sample to Sample Distances in Pig Samples" )

Here is the error generated from this:

Error in check.length("fill") : 
  'gpar' element 'fill' must not be length 0

Any help would be greatly appreciated

Please note that pheatmap is not a Bioconductor package. Having said this, why do you explicitly set colnames(sampleDistMatrix) <- NULL ? I would not be surprised if this is the cause of the error. You rather could add this argument when calling pheatmap: show_colnames = FALSE. See the help pages for pheatmap (type ?pheatmap) for all arguments that can be set (you will see there are many...).